diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 0000000000000000000000000000000000000000..88e34589b7bd2dbc5264bb8f7118c1e2dfb3159c
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,283 @@
+[*]
+charset = utf-8
+end_of_line = crlf
+indent_size = 4
+indent_style = space
+insert_final_newline = false
+max_line_length = 120
+tab_width = 4
+ij_continuation_indent_size = 8
+ij_formatter_off_tag = @formatter:off
+ij_formatter_on_tag = @formatter:on
+ij_formatter_tags_enabled = false
+ij_smart_tabs = false
+ij_wrap_on_typing = false
+
+[*.java]
+ij_java_align_consecutive_assignments = false
+ij_java_align_consecutive_variable_declarations = false
+ij_java_align_group_field_declarations = false
+ij_java_align_multiline_annotation_parameters = false
+ij_java_align_multiline_array_initializer_expression = false
+ij_java_align_multiline_assignment = false
+ij_java_align_multiline_binary_operation = false
+ij_java_align_multiline_chained_methods = false
+ij_java_align_multiline_extends_list = false
+ij_java_align_multiline_for = true
+ij_java_align_multiline_method_parentheses = false
+ij_java_align_multiline_parameters = true
+ij_java_align_multiline_parameters_in_calls = false
+ij_java_align_multiline_parenthesized_expression = false
+ij_java_align_multiline_records = true
+ij_java_align_multiline_resources = true
+ij_java_align_multiline_ternary_operation = false
+ij_java_align_multiline_text_blocks = false
+ij_java_align_multiline_throws_list = false
+ij_java_align_subsequent_simple_methods = false
+ij_java_align_throws_keyword = false
+ij_java_annotation_parameter_wrap = off
+ij_java_array_initializer_new_line_after_left_brace = false
+ij_java_array_initializer_right_brace_on_new_line = false
+ij_java_array_initializer_wrap = off
+ij_java_assert_statement_colon_on_next_line = false
+ij_java_assert_statement_wrap = off
+ij_java_assignment_wrap = off
+ij_java_binary_operation_sign_on_next_line = false
+ij_java_binary_operation_wrap = off
+ij_java_blank_lines_after_anonymous_class_header = 0
+ij_java_blank_lines_after_class_header = 0
+ij_java_blank_lines_after_imports = 1
+ij_java_blank_lines_after_package = 1
+ij_java_blank_lines_around_class = 1
+ij_java_blank_lines_around_field = 0
+ij_java_blank_lines_around_field_in_interface = 0
+ij_java_blank_lines_around_initializer = 1
+ij_java_blank_lines_around_method = 1
+ij_java_blank_lines_around_method_in_interface = 1
+ij_java_blank_lines_before_class_end = 0
+ij_java_blank_lines_before_imports = 1
+ij_java_blank_lines_before_method_body = 0
+ij_java_blank_lines_before_package = 0
+ij_java_block_brace_style = next_line
+ij_java_block_comment_at_first_column = true
+ij_java_call_parameters_new_line_after_left_paren = false
+ij_java_call_parameters_right_paren_on_new_line = false
+ij_java_call_parameters_wrap = off
+ij_java_case_statement_on_separate_line = true
+ij_java_catch_on_new_line = true
+ij_java_class_annotation_wrap = split_into_lines
+ij_java_class_brace_style = next_line
+ij_java_class_count_to_use_import_on_demand = 5
+ij_java_class_names_in_javadoc = 1
+ij_java_do_not_indent_top_level_class_members = false
+ij_java_do_not_wrap_after_single_annotation = false
+ij_java_do_while_brace_force = always
+ij_java_doc_add_blank_line_after_description = true
+ij_java_doc_add_blank_line_after_param_comments = false
+ij_java_doc_add_blank_line_after_return = false
+ij_java_doc_add_p_tag_on_empty_lines = true
+ij_java_doc_align_exception_comments = true
+ij_java_doc_align_param_comments = true
+ij_java_doc_do_not_wrap_if_one_line = false
+ij_java_doc_enable_formatting = true
+ij_java_doc_enable_leading_asterisks = true
+ij_java_doc_indent_on_continuation = false
+ij_java_doc_keep_empty_lines = true
+ij_java_doc_keep_empty_parameter_tag = true
+ij_java_doc_keep_empty_return_tag = true
+ij_java_doc_keep_empty_throws_tag = true
+ij_java_doc_keep_invalid_tags = true
+ij_java_doc_param_description_on_new_line = false
+ij_java_doc_preserve_line_breaks = false
+ij_java_doc_use_throws_not_exception_tag = true
+ij_java_else_on_new_line = true
+ij_java_enum_constants_wrap = off
+ij_java_extends_keyword_wrap = off
+ij_java_extends_list_wrap = off
+ij_java_field_annotation_wrap = split_into_lines
+ij_java_finally_on_new_line = true
+ij_java_for_brace_force = always
+ij_java_for_statement_new_line_after_left_paren = false
+ij_java_for_statement_right_paren_on_new_line = false
+ij_java_for_statement_wrap = off
+ij_java_generate_final_locals = false
+ij_java_generate_final_parameters = false
+ij_java_if_brace_force = always
+ij_java_imports_layout = *,|,javax.**,java.**,|,$*
+ij_java_indent_case_from_switch = true
+ij_java_insert_inner_class_imports = false
+ij_java_insert_override_annotation = true
+ij_java_keep_blank_lines_before_right_brace = 2
+ij_java_keep_blank_lines_between_package_declaration_and_header = 2
+ij_java_keep_blank_lines_in_code = 2
+ij_java_keep_blank_lines_in_declarations = 2
+ij_java_keep_control_statement_in_one_line = true
+ij_java_keep_first_column_comment = true
+ij_java_keep_indents_on_empty_lines = false
+ij_java_keep_line_breaks = true
+ij_java_keep_multiple_expressions_in_one_line = false
+ij_java_keep_simple_blocks_in_one_line = false
+ij_java_keep_simple_classes_in_one_line = false
+ij_java_keep_simple_lambdas_in_one_line = false
+ij_java_keep_simple_methods_in_one_line = false
+ij_java_label_indent_absolute = false
+ij_java_label_indent_size = 0
+ij_java_lambda_brace_style = next_line
+ij_java_layout_static_imports_separately = true
+ij_java_line_comment_add_space = false
+ij_java_line_comment_at_first_column = true
+ij_java_method_annotation_wrap = split_into_lines
+ij_java_method_brace_style = next_line
+ij_java_method_call_chain_wrap = off
+ij_java_method_parameters_new_line_after_left_paren = false
+ij_java_method_parameters_right_paren_on_new_line = false
+ij_java_method_parameters_wrap = off
+ij_java_modifier_list_wrap = false
+ij_java_names_count_to_use_import_on_demand = 3
+ij_java_new_line_after_lparen_in_record_header = false
+ij_java_packages_to_use_import_on_demand = java.awt.*,javax.swing.*
+ij_java_parameter_annotation_wrap = off
+ij_java_parentheses_expression_new_line_after_left_paren = false
+ij_java_parentheses_expression_right_paren_on_new_line = false
+ij_java_place_assignment_sign_on_next_line = false
+ij_java_prefer_longer_names = true
+ij_java_prefer_parameters_wrap = false
+ij_java_record_components_wrap = normal
+ij_java_repeat_synchronized = true
+ij_java_replace_instanceof_and_cast = false
+ij_java_replace_null_check = true
+ij_java_replace_sum_lambda_with_method_ref = true
+ij_java_resource_list_new_line_after_left_paren = false
+ij_java_resource_list_right_paren_on_new_line = false
+ij_java_resource_list_wrap = normal
+ij_java_rparen_on_new_line_in_record_header = false
+ij_java_space_after_closing_angle_bracket_in_type_argument = false
+ij_java_space_after_colon = true
+ij_java_space_after_comma = true
+ij_java_space_after_comma_in_type_arguments = true
+ij_java_space_after_for_semicolon = true
+ij_java_space_after_quest = true
+ij_java_space_after_type_cast = true
+ij_java_space_before_annotation_array_initializer_left_brace = false
+ij_java_space_before_annotation_parameter_list = false
+ij_java_space_before_array_initializer_left_brace = false
+ij_java_space_before_catch_keyword = true
+ij_java_space_before_catch_left_brace = true
+ij_java_space_before_catch_parentheses = true
+ij_java_space_before_class_left_brace = true
+ij_java_space_before_colon = true
+ij_java_space_before_colon_in_foreach = true
+ij_java_space_before_comma = false
+ij_java_space_before_do_left_brace = true
+ij_java_space_before_else_keyword = true
+ij_java_space_before_else_left_brace = true
+ij_java_space_before_finally_keyword = true
+ij_java_space_before_finally_left_brace = true
+ij_java_space_before_for_left_brace = true
+ij_java_space_before_for_parentheses = true
+ij_java_space_before_for_semicolon = false
+ij_java_space_before_if_left_brace = true
+ij_java_space_before_if_parentheses = true
+ij_java_space_before_method_call_parentheses = false
+ij_java_space_before_method_left_brace = true
+ij_java_space_before_method_parentheses = false
+ij_java_space_before_opening_angle_bracket_in_type_parameter = false
+ij_java_space_before_quest = true
+ij_java_space_before_switch_left_brace = true
+ij_java_space_before_switch_parentheses = true
+ij_java_space_before_synchronized_left_brace = true
+ij_java_space_before_synchronized_parentheses = true
+ij_java_space_before_try_left_brace = true
+ij_java_space_before_try_parentheses = true
+ij_java_space_before_type_parameter_list = false
+ij_java_space_before_while_keyword = true
+ij_java_space_before_while_left_brace = true
+ij_java_space_before_while_parentheses = true
+ij_java_space_inside_one_line_enum_braces = false
+ij_java_space_within_empty_array_initializer_braces = false
+ij_java_space_within_empty_method_call_parentheses = false
+ij_java_space_within_empty_method_parentheses = false
+ij_java_spaces_around_additive_operators = true
+ij_java_spaces_around_assignment_operators = true
+ij_java_spaces_around_bitwise_operators = true
+ij_java_spaces_around_equality_operators = true
+ij_java_spaces_around_lambda_arrow = true
+ij_java_spaces_around_logical_operators = true
+ij_java_spaces_around_method_ref_dbl_colon = false
+ij_java_spaces_around_multiplicative_operators = true
+ij_java_spaces_around_relational_operators = true
+ij_java_spaces_around_shift_operators = true
+ij_java_spaces_around_type_bounds_in_type_parameters = true
+ij_java_spaces_around_unary_operator = true
+ij_java_spaces_within_angle_brackets = true
+ij_java_spaces_within_annotation_parentheses = true
+ij_java_spaces_within_array_initializer_braces = true
+ij_java_spaces_within_braces = true
+ij_java_spaces_within_brackets = true
+ij_java_spaces_within_cast_parentheses = true
+ij_java_spaces_within_catch_parentheses = true
+ij_java_spaces_within_for_parentheses = true
+ij_java_spaces_within_if_parentheses = true
+ij_java_spaces_within_method_call_parentheses = true
+ij_java_spaces_within_method_parentheses = true
+ij_java_spaces_within_parentheses = true
+ij_java_spaces_within_switch_parentheses = true
+ij_java_spaces_within_synchronized_parentheses = true
+ij_java_spaces_within_try_parentheses = true
+ij_java_spaces_within_while_parentheses = true
+ij_java_special_else_if_treatment = true
+ij_java_subclass_name_suffix = Impl
+ij_java_ternary_operation_signs_on_next_line = false
+ij_java_ternary_operation_wrap = off
+ij_java_test_name_suffix = Test
+ij_java_throws_keyword_wrap = off
+ij_java_throws_list_wrap = off
+ij_java_use_external_annotations = false
+ij_java_use_fq_class_names = false
+ij_java_use_relative_indents = false
+ij_java_use_single_class_imports = true
+ij_java_variable_annotation_wrap = off
+ij_java_visibility = public
+ij_java_while_brace_force = always
+ij_java_while_on_new_line = false
+ij_java_wrap_comments = false
+ij_java_wrap_first_method_in_call_chain = false
+ij_java_wrap_long_lines = false
+
+[*.properties]
+ij_properties_align_group_field_declarations = false
+ij_properties_keep_blank_lines = false
+ij_properties_key_value_delimiter = equals
+ij_properties_spaces_around_key_value_delimiter = false
+
+[.editorconfig]
+ij_editorconfig_align_group_field_declarations = false
+ij_editorconfig_space_after_colon = false
+ij_editorconfig_space_after_comma = true
+ij_editorconfig_space_before_colon = false
+ij_editorconfig_space_before_comma = false
+ij_editorconfig_spaces_around_assignment_operators = true
+
+[{*.ant,*.fxml,*.jhm,*.jnlp,*.jrxml,*.jspx,*.pom,*.rng,*.tagx,*.tld,*.wsdl,*.xml,*.xsd,*.xsl,*.xslt,*.xul}]
+ij_xml_align_attributes = true
+ij_xml_align_text = false
+ij_xml_attribute_wrap = normal
+ij_xml_block_comment_at_first_column = true
+ij_xml_keep_blank_lines = 2
+ij_xml_keep_indents_on_empty_lines = false
+ij_xml_keep_line_breaks = true
+ij_xml_keep_line_breaks_in_text = true
+ij_xml_keep_whitespaces = false
+ij_xml_keep_whitespaces_around_cdata = preserve
+ij_xml_keep_whitespaces_inside_cdata = false
+ij_xml_line_comment_at_first_column = true
+ij_xml_space_after_tag_name = false
+ij_xml_space_around_equals_in_attribute = false
+ij_xml_space_inside_empty_tag = false
+ij_xml_text_wrap = normal
+ij_xml_use_custom_settings = false
+
+[{*.yaml,*.yml}]
+indent_size = 2
+ij_yaml_keep_indents_on_empty_lines = false
+ij_yaml_keep_line_breaks = true
diff --git a/README.md b/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..ed1286ba3c280b2164817d93e514acfba090e24b
--- /dev/null
+++ b/README.md
@@ -0,0 +1,69 @@
+# zellige-core
+
+
+
+ ## Workflow
+
+- I. Input of the image.
+
+ - The image has to be a z-stack.
+
+
+ - II. Pretreatment of the image.
+
+ - Conversion of pixel values into FloatType
+
+ - Image denoising with an anisotropic gaussian convolution
+
+ - Normalization of the histogram (pixel value between 0 and 255).
+
+- III. Local maximum search and selection according to user specified minimum threshold parameter (percent) and dilation (sigma).
+
+ - Local maximum detection using partial derivative
+
+ - Grid of local thresholds using Otsu thresholding method.
+
+ - Maxima selection according to local thresholds
+
+ - Dilatation of the resulting image
+
+ - New local maximum detection due to previous smoothing
+
+ - Conversion of the coordinates found into a 2D Pixels array
+
+
+
+ - IV. Construction of the OS in dimension Y */
+
+ - Construction of OS .
+
+- V. Construction of the surfaces in dimension X.*/
+
+ Construction of Surface. Merging of those if necessary.
+
+- VI. Reconstruction of the tempSurface found in dimension 1.
+
+ - Construction of the previous Surface objects in the other dimension if they contain duplicates.
+
+ Merging if necessary.
+
+
+ - VII. Production of the height map and referenceSurface according to the delta.
+
+## Build
+
+````
+
+ mvn clean install
+
+ ````
+
+## Usage
+
+````
+
+````
+
+## Pipelines
+
+https://gitlab.pasteur.fr/ctrebeau/zellige-core/-/pipelines
\ No newline at end of file
diff --git a/src/main/java/StartingOSStats.java b/src/main/java/StartingOSStats.java
index 9c0c4c3fe8c0765ec3df25a9884e4b1fffe8879b..1217020f467ce7d90a2e76a27056c09b44bac865 100644
--- a/src/main/java/StartingOSStats.java
+++ b/src/main/java/StartingOSStats.java
@@ -1,5 +1,7 @@
-import fr.pasteur.ida.zellige.surfaceConstruction.construction.SurfacesExtraction;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSE;
+import fr.pasteur.ida.zellige.surfaceConstruction.parameters.AdvancedUserParameters;
+import fr.pasteur.ida.zellige.surfaceConstruction.construction.ReferenceSurfaceExtraction;
+import fr.pasteur.ida.zellige.surfaceConstruction.parameters.UserParameters;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ose.OSE;
import fr.pasteur.ida.zellige.utils.TestMIP;
import ij.IJ;
import ij.ImageJ;
@@ -88,9 +90,8 @@ public class StartingOSStats
int delta = Integer.parseInt( args[ 7 ] );
/* End of parameters. */
-
-
- /* End of Print parameters.*/
+ UserParameters userParameters = new UserParameters( amplitude, otsu, sigmas, delta, "MIP" );
+ AdvancedUserParameters advancedUserParameters = new AdvancedUserParameters( k1, percent1, k2, percent2 );
IJ.log("Type: "+ imgPlus.firstElement().getClass().toGenericString());
@@ -98,10 +99,7 @@ public class StartingOSStats
{
ImageJFunctions.show( stackImage, "original" );
ImageJFunctions.show( TestMIP.findMIP( stackImage, stackImage.factory() ), "MIP" );
-
-
- SurfacesExtraction.extract(stackImage, stackImage.factory(),amplitude, otsu, sigmas, false, delta, false,
- false, true, "MIP", k1, percent1, k2, percent2);
+ new ReferenceSurfaceExtraction<>( stackImage, stackImage.factory(),userParameters, advancedUserParameters );
}
else
{
diff --git a/src/main/java/SurfacesExtractionAnalyse.java b/src/main/java/SurfacesExtractionAnalyse.java
index ed2a32fd47b36d1083a6653e2e3c833d44c645b9..e37a8e35963a6dfec8110fc16d49c1b07b779020 100644
--- a/src/main/java/SurfacesExtractionAnalyse.java
+++ b/src/main/java/SurfacesExtractionAnalyse.java
@@ -1,30 +1,3 @@
-import fr.pasteur.ida.zellige.exception.FirstRoundConstructionException;
-import fr.pasteur.ida.zellige.exception.NoSurfaceFoundException;
-import fr.pasteur.ida.zellige.jzy3D.LocalMaximumsDisplay;
-import fr.pasteur.ida.zellige.jzy3D.OSDisplay;
-import fr.pasteur.ida.zellige.jzy3D.SurfaceDisplay;
-import fr.pasteur.ida.zellige.surfaceConstruction.construction.OSConstruction;
-import fr.pasteur.ida.zellige.surfaceConstruction.construction.SurfacesReconstruction;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.Surface;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSE;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSEStartingStatus;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSList;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.surfaceLine.SurfaceLine;
-import fr.pasteur.ida.zellige.utils.*;
-import io.scif.img.IO;
-import io.scif.img.SCIFIOImgPlus;
-import net.imglib2.img.Img;
-import net.imglib2.img.display.imagej.ImageJFunctions;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.logic.BitType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.type.numeric.integer.UnsignedShortType;
-import org.jzy3d.analysis.AnalysisLauncher;
-
-import java.util.ArrayList;
-
-
public class SurfacesExtractionAnalyse
{
// public static < T extends RealType < T > & NativeType < T > > void main( String[] args )
diff --git a/src/main/java/fr/pasteur/ida/zellige/command/ZelligeCommand.java b/src/main/java/fr/pasteur/ida/zellige/command/ZelligeCommand.java
deleted file mode 100644
index b4768efec9c7b1bb60c775c72a30d340e7104314..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/command/ZelligeCommand.java
+++ /dev/null
@@ -1,93 +0,0 @@
-package fr.pasteur.ida.zellige.command;
-
-import ij.IJ;
-import net.imagej.Dataset;
-import net.imagej.ImgPlus;
-import net.imagej.display.ImageDisplayService;
-import net.imagej.ops.OpService;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.util.Util;
-import org.scijava.ItemIO;
-import org.scijava.command.ContextCommand;
-import org.scijava.log.LogService;
-import org.scijava.plugin.Parameter;
-import org.scijava.plugin.Plugin;
-
-import java.util.ArrayList;
-
-@Plugin ( type = ZelligeCommand.class, name = "Zellige", menuPath = "Plugins > Process > Zellige" )
-public class ZelligeCommand< T extends RealType < T > & NativeType < T > > extends ContextCommand
-{
-
- @Parameter
- private ImageDisplayService imageDisplayService;
-
- @Parameter
- private LogService logService;
-
- @Parameter
- protected OpService ops;
-
- @Parameter
- private int sigma;
-
- @Parameter
- private int localThreshold;
-
- @Parameter
- private int globalThreshold;
-
- @Parameter
- private int delta;
-
- @Parameter(type = ItemIO.OUTPUT)
- ArrayList < RandomAccessibleInterval < T > > surfaces;
-
- @Override
- public void run()
- {
- /*
- * Get current dataset.
- */
-
- Dataset dataset = imageDisplayService.getActiveDataset();
- if ( null == dataset )
- {
- logService.error( "Please open an image before running Zellige." );
- return;
- }
- /*
- * Wrap it into an ImgLib2 'Plus' image.
- */
- @SuppressWarnings( "unchecked" )
- ImgPlus < T > img = ( ImgPlus< T > ) dataset.getImgPlus();
-
- long[] dims = new long[dataset.numDimensions()];
- dataset.dimensions(dims);
-
- IJ.log( "Zellige received the image: " + img.getName() );
- IJ.log( "Size: " + Util.printInterval( img ) );
- IJ.log( "Type: " + img.firstElement().getClass().toGenericString() );
- IJ.log( "Dimensionality: " + img.numDimensions() + "D" );
- for ( int d = 0; d < img.numDimensions(); d++ )
- IJ.log( " - dimension " + d + ": [" + img.axis( d ).type() + "], 1 unit = " + img.averageScale( d ) + " " + img.axis( d ).unit() );
- if ( img.numDimensions() == 3 )// Is it a stack ?
- {
-// SurfacesExtraction <T > extraction =
-// new SurfacesExtraction <>( img, localThreshold, globalThreshold, sigma, delta );
-// surfaces = extraction.extract();
- }
- else
- {
- IJ.log( " This image has to be a z-stack ! " );
- }
- IJ.log(" Number of surfaces found : " + surfaces.size());
- }
-}
-
-
-
-
-
diff --git a/src/main/java/fr/pasteur/ida/zellige/command/ZelligeCommand2.java b/src/main/java/fr/pasteur/ida/zellige/command/ZelligeCommand2.java
deleted file mode 100644
index 30575cb21b87348cbbfb9edc1f5a945bc3051774..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/command/ZelligeCommand2.java
+++ /dev/null
@@ -1,18 +0,0 @@
-package fr.pasteur.ida.zellige.command;
-
-import fr.pasteur.ida.zellige.gui.ZelligeController;
-import org.scijava.command.ContextCommand;
-import org.scijava.plugin.Plugin;
-
-
-@Plugin( type = fr.pasteur.ida.zellige.command.ZelligeCommand.class, name = "Zellige", menuPath = "Plugins > Process > Zellige" )
-public class ZelligeCommand2 extends ContextCommand
-{
-
-
- @Override
- public void run()
- {
- new ZelligeController( context() );
- }
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/command/ZelligePluginTestDrive.java b/src/main/java/fr/pasteur/ida/zellige/command/ZelligePluginTestDrive.java
deleted file mode 100644
index 32e3f46b614ef10cbd71ebb2e67619c39d837f72..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/command/ZelligePluginTestDrive.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package fr.pasteur.ida.zellige.command;
-
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.FileSystems;
-
-
-import net.imagej.ImageJ;
-
-public class ZelligePluginTestDrive
-{
-
- public static void main( String[] args ) throws IOException
- {
- String currentFolder = FileSystems.getDefault()
- .getPath( "" )
- .toAbsolutePath()
- .toString();
- String imageFilePath = "doc/STK_crop.tif";
-
- // Launch ImageJ.
- ImageJ ij = new ImageJ();
- ij.launch( args );
-
- // Load the image.
- Object obj = ij.io().open( new File( currentFolder, imageFilePath ).getAbsolutePath() );
-
- // Display it.
- ij.ui().show( obj );
-
- ij.command().run( ZelligeCommand2.class, true );
- }
-
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/AdvancedSettings.form b/src/main/java/fr/pasteur/ida/zellige/gui/AdvancedSettings.form
deleted file mode 100644
index ec7eb2db8b73c480f630829ab6e7a11c63defa7c..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/gui/AdvancedSettings.form
+++ /dev/null
@@ -1,203 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<form xmlns="http://www.intellij.com/uidesigner/form/" version="1" bind-to-class="fr.pasteur.ida.zellige.gui.AdvancedSettings">
- <grid id="cbd77" binding="contentPane" layout-manager="GridLayoutManager" row-count="2" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="10" left="10" bottom="10" right="10"/>
- <constraints>
- <xy x="48" y="54" width="436" height="204"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="94766" layout-manager="GridLayoutManager" row-count="1" column-count="2" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="1" column="0" row-span="1" col-span="1" vsize-policy="1" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <hspacer id="98af6">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="1" hsize-policy="6" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
- </constraints>
- </hspacer>
- <grid id="9538f" layout-manager="GridLayoutManager" row-count="1" column-count="2" same-size-horizontally="true" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="e7465" class="javax.swing.JButton" binding="buttonOK">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="OK"/>
- </properties>
- </component>
- <component id="5723f" class="javax.swing.JButton" binding="buttonCancel">
- <constraints>
- <grid row="0" column="1" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="Cancel"/>
- </properties>
- </component>
- </children>
- </grid>
- </children>
- </grid>
- <grid id="e3588" layout-manager="GridLayoutManager" row-count="2" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="6c1a9" binding="panel1" default-binding="true" layout-manager="GridLayoutManager" row-count="3" column-count="2" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="1" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="827a0" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="79d5c" class="javax.swing.JLabel">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="0" anchor="8" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="OS minimum size"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="81448" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="bcc3f" class="fr.pasteur.ida.zellige.gui.ZSpinner" binding="osMinimumSize" custom-create="true" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children/>
- </grid>
- </children>
- </grid>
- <grid id="1f74d" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="1" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="4f849" class="javax.swing.JLabel">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="0" anchor="8" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="First round construction"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="7357a" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="1" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="c4271" class="fr.pasteur.ida.zellige.gui.ZSpinner" binding="firstRound" custom-create="true" default-binding="true" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children/>
- </grid>
- </children>
- </grid>
- <grid id="df249" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="2" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="5f03f" class="javax.swing.JLabel">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="0" anchor="8" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="Second round construction"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="b507b" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="2" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="71495" class="fr.pasteur.ida.zellige.gui.ZSpinner" binding="secondRound" custom-create="true" default-binding="true" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children/>
- </grid>
- </children>
- </grid>
- </children>
- </grid>
- <grid id="9aaf0" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="cb7e3" class="javax.swing.JLabel">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="0" anchor="8" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="OS minimum size"/>
- </properties>
- </component>
- </children>
- </grid>
- </children>
- </grid>
- </children>
- </grid>
-</form>
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/AdvancedSettings.java b/src/main/java/fr/pasteur/ida/zellige/gui/AdvancedSettings.java
deleted file mode 100644
index 34d2a93ec9b5fe8fddb25fd1a734cab52746cf73..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/gui/AdvancedSettings.java
+++ /dev/null
@@ -1,90 +0,0 @@
-package fr.pasteur.ida.zellige.gui;
-
-import javax.swing.*;
-import java.awt.event.*;
-
-public class AdvancedSettings extends JDialog
-{
- private JPanel contentPane;
- private JButton buttonOK;
- private JButton buttonCancel;
- private JPanel panel1;
- private ZSpinner firstRound;
- private ZSpinner secondRound;
- private ZSpinner osMinimumSize;
-
- public AdvancedSettings()
- {
- setContentPane( contentPane );
- setModal( true );
- getRootPane().setDefaultButton( buttonOK );
-
- buttonOK.addActionListener( new ActionListener()
- {
- public void actionPerformed( ActionEvent e )
- {
- onOK();
- }
- } );
-
- buttonCancel.addActionListener( new ActionListener()
- {
- public void actionPerformed( ActionEvent e )
- {
- onCancel();
- }
- } );
-
- // call onCancel() when cross is clicked
- setDefaultCloseOperation( DO_NOTHING_ON_CLOSE );
- addWindowListener( new WindowAdapter()
- {
- public void windowClosing( WindowEvent e )
- {
- onCancel();
- }
- } );
-
- // call onCancel() on ESCAPE
- contentPane.registerKeyboardAction( new ActionListener()
- {
- public void actionPerformed( ActionEvent e )
- {
- onCancel();
- }
- }, KeyStroke.getKeyStroke( KeyEvent.VK_ESCAPE, 0 ), JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT );
- this.pack();
-// this.setVisible( false );
- }
-
- private void createUIComponents()
- {
- firstRound = new ZSpinner( "first round construction value", 0, 2000, 70, 10 );
- firstRound.setDefaultRange( 20, 70 );
- secondRound = new ZSpinner( "second round construction value", 0, 2000, 70, 10 );
- secondRound.setDefaultRange( 20, 70 );
- osMinimumSize = new ZSpinner( "OS Minimum size", 1, 1000, 3, 1 );
- osMinimumSize.setDefaultRange( 2, 30 );
-
- }
-
- private void onOK()
- {
- // add your code here
- dispose();
- }
-
- private void onCancel()
- {
- // add your code here if necessary
- dispose();
- }
-
- public static void main( String[] args )
- {
- AdvancedSettings dialog = new AdvancedSettings();
- dialog.pack();
- dialog.setVisible( true );
- System.exit( 0 );
- }
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/Settings.form b/src/main/java/fr/pasteur/ida/zellige/gui/Settings.form
deleted file mode 100644
index a6a3eccb8d252c510ba9999db858fc6a04caafc7..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/gui/Settings.form
+++ /dev/null
@@ -1,439 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<form xmlns="http://www.intellij.com/uidesigner/form/" version="1" bind-to-class="fr.pasteur.ida.zellige.gui.Settings">
- <grid id="27dc6" binding="panel" layout-manager="GridLayoutManager" row-count="2" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="20" left="20" bottom="20" right="20"/>
- <constraints>
- <xy x="20" y="20" width="362" height="535"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="2525f" layout-manager="GridLayoutManager" row-count="2" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="a5b1b" layout-manager="FlowLayout" hgap="5" vgap="5" flow-align="1">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="78478" class="javax.swing.JLabel">
- <constraints/>
- <properties>
- <text value="Surface extraction settings"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="3c75" layout-manager="GridLayoutManager" row-count="5" column-count="2" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="1" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="59c6e" layout-manager="GridLayoutManager" row-count="1" column-count="2" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="4" column="0" row-span="1" col-span="2" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="f48c3" class="javax.swing.JButton" binding="advancedSettingsButton" default-binding="true">
- <constraints>
- <grid row="0" column="1" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="Advanced settings"/>
- </properties>
- </component>
- <hspacer id="60dae">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="1" hsize-policy="6" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
- </constraints>
- </hspacer>
- </children>
- </grid>
- <grid id="fc361" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="4" fill="2" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="60740" class="javax.swing.JLabel">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="0" anchor="8" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="Blur size"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="d6c7d" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="1" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="c45a6" class="javax.swing.JLabel">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="0" anchor="4" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="Local threshold"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="936f6" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="2" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="391b8" class="javax.swing.JLabel">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="0" anchor="4" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="Global threshold"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="c7b13" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="72ed3" class="fr.pasteur.ida.zellige.gui.ZSpinner" binding="blurSpinner" custom-create="true" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children/>
- </grid>
- </children>
- </grid>
- <grid id="798a9" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="1" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="c82b8" class="fr.pasteur.ida.zellige.gui.ZSpinner" binding="localThresholdSpinner" custom-create="true">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- </component>
- </children>
- </grid>
- <grid id="b25ed" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="2" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="2b274" class="fr.pasteur.ida.zellige.gui.ZSpinner" binding="globalThresholdSpinner" custom-create="true">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- </component>
- </children>
- </grid>
- <grid id="34c04" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="3" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="d065f" class="javax.swing.JLabel">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="0" anchor="4" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="Delta"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="e787a" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="3" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="549c1" class="fr.pasteur.ida.zellige.gui.ZSpinner" binding="deltaSpinner" custom-create="true">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- </component>
- </children>
- </grid>
- </children>
- </grid>
- </children>
- </grid>
- <grid id="6ecf0" layout-manager="GridLayoutManager" row-count="4" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="1" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="d6313" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="3" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="7c19b" class="javax.swing.JButton" binding="runZelligeButton" default-binding="true">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="Run Zellige"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="fbf72" layout-manager="FlowLayout" hgap="5" vgap="5" flow-align="1">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="b6c35" class="javax.swing.JLabel">
- <constraints/>
- <properties>
- <text value="Output Settings"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="beadd" layout-manager="GridLayoutManager" row-count="3" column-count="2" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="1" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="e3a82" layout-manager="FlowLayout" hgap="5" vgap="5" flow-align="1">
- <constraints>
- <grid row="1" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="4" fill="2" indent="0" use-parent-layout="false">
- <preferred-size width="50" height="20"/>
- </grid>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="ca880" class="javax.swing.JLabel">
- <constraints/>
- <properties>
- <text value="Extracted stack"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="a6c85" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="2" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false">
- <preferred-size width="50" height="24"/>
- </grid>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="2b021" class="javax.swing.JLabel">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="0" anchor="4" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="Projection"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="6ea90" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="1" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false">
- <preferred-size width="50" height="24"/>
- </grid>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="efaed" class="javax.swing.JCheckBox" binding="extractedStack">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="8" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value=""/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="d89e9" layout-manager="GridLayoutManager" row-count="1" column-count="2" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="2" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false">
- <preferred-size width="145" height="24"/>
- </grid>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="f900f" class="javax.swing.JCheckBox" binding="projection">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="8" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value=""/>
- </properties>
- </component>
- <component id="ec4fb" class="javax.swing.JComboBox" binding="projectionType" custom-create="true">
- <constraints>
- <grid row="0" column="1" row-span="1" col-span="1" vsize-policy="0" hsize-policy="2" anchor="8" fill="1" indent="0" use-parent-layout="false">
- <preferred-size width="146" height="30"/>
- </grid>
- </constraints>
- <properties>
- <enabled value="false"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="44706" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="b2ef" class="javax.swing.JLabel">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="0" anchor="4" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="Zmap"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="d8eaf" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false">
- <preferred-size width="50" height="-1"/>
- </grid>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="32059" class="javax.swing.JCheckBox" binding="zMap" default-binding="true">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="8" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value=""/>
- </properties>
- </component>
- </children>
- </grid>
- </children>
- </grid>
- <grid id="60958" layout-manager="GridLayoutManager" row-count="1" column-count="2" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="2" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <grid id="1defa" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false">
- <preferred-size width="50" height="24"/>
- </grid>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="df956" class="javax.swing.JLabel">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="0" anchor="4" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <text value="Height map"/>
- </properties>
- </component>
- </children>
- </grid>
- <grid id="4c1e1" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
- <margin top="0" left="0" bottom="0" right="0"/>
- <constraints>
- <grid row="0" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false">
- <preferred-size width="145" height="24"/>
- </grid>
- </constraints>
- <properties/>
- <border type="none"/>
- <children>
- <component id="f540f" class="javax.swing.JCheckBox" binding="HeightMap">
- <constraints>
- <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="8" fill="0" indent="0" use-parent-layout="false"/>
- </constraints>
- <properties>
- <enabled value="false"/>
- <text value=""/>
- </properties>
- </component>
- </children>
- </grid>
- </children>
- </grid>
- </children>
- </grid>
- </children>
- </grid>
-</form>
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/Settings.java b/src/main/java/fr/pasteur/ida/zellige/gui/Settings.java
deleted file mode 100644
index 642d8714840c1f6c10f8f9152f6f2e989c45742a..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/gui/Settings.java
+++ /dev/null
@@ -1,107 +0,0 @@
-package fr.pasteur.ida.zellige.gui;
-
-import javax.swing.*;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
-public class Settings
-{
- private JButton advancedSettingsButton;
- private JButton runZelligeButton;
- private JComboBox <String> projectionType;
- private JCheckBox extractedStack;
- private JCheckBox HeightMap;
- private JCheckBox projection;
- private ZSpinner blurSpinner;
- private ZSpinner localThresholdSpinner;
- private ZSpinner globalThresholdSpinner;
- private ZSpinner deltaSpinner;
- private JCheckBox zMap;
- private JPanel panel;
-
-
- public Settings( )
- {
-
- }
-
-
-
-
- private void createUIComponents()
- {
- this.blurSpinner = new ZSpinner("blur value", 0, 50, 15, 1 );
- this.blurSpinner.setDefaultRange( 5, 20 );
- this.localThresholdSpinner = new ZSpinner( "local threshold value",0, 100, 70, 5 );
- this.localThresholdSpinner.setDefaultRange( 0 , 90);
- this.globalThresholdSpinner = new ZSpinner("global threshold value", 0, 100, 30, 5 );
- this.globalThresholdSpinner.setDefaultRange( 0, 50 );
- this.deltaSpinner = new ZSpinner("delta value", 0, 50, 1, 1 );
- this.deltaSpinner.setDefaultRange( 0, 3 );
- String[] strings = new String[]{"MIP", "Minimum Intensity", "Median", "FastSME", "Element 4", "Element 5"};
- this.projectionType = new JComboBox<>(strings);
- }
-
-
- public JButton getRunZelligeButton()
- {
- return runZelligeButton;
- }
-
- public JComboBox <String> getProjectionType()
- {
- return projectionType;
- }
-
- public JCheckBox getZMap()
- {
- return zMap;
- }
-
- public JCheckBox getExtractedStack()
- {
- return extractedStack;
- }
-
- public JCheckBox getHeightMap()
- {
- return HeightMap;
- }
-
- public JCheckBox getProjection()
- {
- return projection;
- }
-
- public ZSpinner getBlurSpinner()
- {
- return blurSpinner;
- }
-
- public ZSpinner getLocalThresholdSpinner()
- {
- return localThresholdSpinner;
- }
-
- public ZSpinner getGlobalThresholdSpinner()
- {
- return globalThresholdSpinner;
- }
-
- public ZSpinner getDeltaSpinner()
- {
- return deltaSpinner;
- }
-
- public JButton getAdvancedSettingsButton()
- {
- return advancedSettingsButton;
- }
-
- public JPanel getPanel()
- {
- return panel;
- }
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ZSpinner.java b/src/main/java/fr/pasteur/ida/zellige/gui/ZSpinner.java
deleted file mode 100644
index acf9a3c164eaf884dc822a5189e5d19a42c26c76..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/gui/ZSpinner.java
+++ /dev/null
@@ -1,62 +0,0 @@
-package fr.pasteur.ida.zellige.gui;
-
-
-
-import javax.swing.*;
-import java.awt.*;
-
-public class ZSpinner extends JSpinner
-{
- private int minDefaultValue = -1;
- private int maxDefaultValue = -1;
- private final String name;
-
- public ZSpinner(String name, int min, int max, int value, int step)
- {
- super(new SpinnerNumberModel(value, min, max, step));
- this.name = name;
- this.setPreferredSize( new Dimension(100, 20) );
-
- }
-
-//TODO color range not working
- public void setRangeColor()
- {
- if (getTextValue() < minDefaultValue || getTextValue()> maxDefaultValue)
- {
- this.getEditor().setBackground( Color.RED );
- }
- else
- {
- this.getEditor().setForeground( Color.BLACK );
- }
- }
-
- public int getTextValue() {
- JComponent editor = this.getEditor();
- if (editor instanceof JSpinner.DefaultEditor) {
- JFormattedTextField formattedTextField = ((JSpinner.DefaultEditor) editor ).getTextField();
- try
- {
- int value = Integer.parseInt( formattedTextField.getText().trim());
- System.out.println(value);
- return value;
- }
- catch ( NumberFormatException nfe )
- {
- JOptionPane.showMessageDialog(null, "The "+ name + " is not an integer.",
- "Error Message", JOptionPane.ERROR_MESSAGE);
-
- }
- }
- return -1;
- }
-
-
-
- public void setDefaultRange(int min, int max)
- {
- this.minDefaultValue = min;
- this.maxDefaultValue = max;
- }
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/ZelligeController.java b/src/main/java/fr/pasteur/ida/zellige/gui/ZelligeController.java
deleted file mode 100644
index fbcb55ca25aa185c012a915e1c764fed26036934..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/gui/ZelligeController.java
+++ /dev/null
@@ -1,195 +0,0 @@
-package fr.pasteur.ida.zellige.gui;
-import fr.pasteur.ida.zellige.surfaceConstruction.construction.SurfacesExtraction;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
-import ij.IJ;
-import net.imagej.ImgPlus;
-import net.imagej.display.ImageDisplayService;
-import net.imagej.ops.OpService;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.util.Util;
-import org.scijava.Context;
-import org.scijava.log.LogService;
-
-import net.imagej.Dataset;
-
-import javax.swing.*;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.function.Supplier;
-
-
-
-public class ZelligeController implements ChangeListener, ActionListener
-{
- private final Context context;
- private ImageDisplayService imageDisplayService;
-
- private final Settings settings;
- private final AdvancedSettings advancedSettings;
-
- private JButton advancedSettingsButton;
- private JButton runZelligeButton;
- private JCheckBox zMap;
- private JComboBox<String> projectionType;
- private JCheckBox extractedStack;
- private JCheckBox HeightMap;
- private JCheckBox projection;
- private ZSpinner blurSpinner;
- private ZSpinner localThresholdSpinner;
- private ZSpinner globalThresholdSpinner;
- private ZSpinner deltaSpinner;
-
-// private Cancelable cancelable;
-
- private final OpService ops;
-
- private final LogService logService;
-
- public ZelligeController( Context context )
- {
- this.context = context;
- this.ops = context.getService( OpService.class );
- this.logService = context.getService( LogService.class );
-
- final ImageDisplayService imageDisplayService = context.getService( ImageDisplayService.class );
- final Supplier< Dataset > datasetSupplier = () -> imageDisplayService.getActiveDataset();
-
- this.advancedSettings = new AdvancedSettings();
- this.settings = new Settings();
-
- this.set();
-
-
- final JFrame frame = new JFrame("Zellige");
- frame.setLocationByPlatform( true );
- frame.setLocationRelativeTo( null );
- frame.getContentPane().add( settings.getPanel() );
- frame.pack();
- frame.setVisible( true );
- frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-
-
- }
-
- @Override
- public void stateChanged( ChangeEvent e )
- {
- if (e.getSource() instanceof ZSpinner )
- {
- ZSpinner zSpinner = ( ZSpinner ) e.getSource();
- zSpinner.setRangeColor();
- }
- }
-
- @Override
- public void actionPerformed( ActionEvent e )
- {
- if (e.getSource() instanceof JButton )
- {
- if (e.getSource().equals( this.advancedSettingsButton ))
- {
- this.advancedSettings.setVisible( true );
- }
- else if (e.getSource().equals( this.runZelligeButton ))
- {
- runZellige();
- }
- }
- else if (e.getSource().equals( this.projection ))// Projection type display only if the projection checkBox is selected
- {
- this.projectionType.setEnabled( this.projection.isSelected() );
- this.HeightMap.setEnabled( this.projection.isSelected() );
- }
-
- else if ( e.getSource().equals( this.projectionType ))
- {
- if ( this.projectionType.getSelectedItem().toString().trim().equals( "MIP")
- ||this.projectionType.getSelectedItem() == "Minimum Intensity" )
- {
- this.HeightMap.setEnabled( true );
- }
- else{
- this.HeightMap.setEnabled( false );
- }
- }
- }
-
-
- public void set()
- {
-
- this.blurSpinner = this.settings.getBlurSpinner();
- this.blurSpinner.addChangeListener( this );
- this.localThresholdSpinner = this.settings.getLocalThresholdSpinner();
- this.localThresholdSpinner.addChangeListener( this );
- this.globalThresholdSpinner = this.settings.getGlobalThresholdSpinner();
- this.globalThresholdSpinner.addChangeListener( this );
- this.deltaSpinner = this.settings.getDeltaSpinner();
- this.deltaSpinner.addChangeListener( this );
- this.extractedStack = this.settings.getExtractedStack();
- this.HeightMap = this.settings.getHeightMap();
- this.projection = this.settings.getProjection();
- this.projection.addActionListener( this );
- this.projectionType = this.settings.getProjectionType();
- this.projectionType.addActionListener( this );
- this.zMap = this.settings.getZMap();
- this.advancedSettingsButton = this.settings.getAdvancedSettingsButton();
- this.advancedSettingsButton.addActionListener( this );
- this.runZelligeButton = this.settings.getRunZelligeButton();
- this.runZelligeButton.addActionListener( this );
- }
-
- public< T extends RealType< T > & NativeType< T > > void runZellige()
- {
-
- final ImageDisplayService imageDisplayService = context.getService( ImageDisplayService.class );
- final Supplier< Dataset > datasetSupplier = () -> imageDisplayService.getActiveDataset();
- Dataset dataset = imageDisplayService.getActiveDataset();
- if ( null == dataset )
- {
- logService.error( "Please open an image before running Zellige." );
- return;
- }
- /*
- * Wrap it into an ImgLib2 'Plus' image.
- */
- @SuppressWarnings( "unchecked" )
- ImgPlus< T > stackImage = ( ImgPlus< T > ) datasetSupplier.get().getImgPlus();
-
- long[] dims = new long[dataset.numDimensions()];
- dataset.dimensions(dims);
-
- IJ.log( "Zellige received the image: " + stackImage.getName() );
- IJ.log( "Size: " + Util.printInterval( stackImage ) );
- IJ.log( "Type: " + stackImage.firstElement().getClass().toGenericString() );
- IJ.log( "Dimensionality: " + stackImage.numDimensions() + "D" );
- for ( int d = 0; d < stackImage.numDimensions(); d++ )
- IJ.log( " - dimension " + d + ": [" + stackImage.axis( d ).type() + "], 1 unit = " + stackImage.averageScale( d ) + " " + stackImage.axis( d ).unit() );
- if ( stackImage.numDimensions() == 3 )// Is it a stack ?
- {
-
-
- int localThreshold = localThresholdSpinner.getTextValue();
- int globalThreshold = globalThresholdSpinner.getTextValue();
- int sigma = blurSpinner.getTextValue();
- int delta = deltaSpinner.getTextValue();
- boolean zMapDisplay = this.zMap.isSelected();
- boolean extractedStackDisplay = this.extractedStack.isSelected();
- boolean heightMapDisplay = this.HeightMap.isSelected();
- boolean projectionDisplay = this.projection.isSelected();
- String projectionSelection = ( String ) this.projectionType.getEditor().getItem();
-// SurfacesExtraction.extract(stackImage, globalThreshold, sigma, maximums,
-// zMapDisplay, delta, extractedStackDisplay,
-// heightMapDisplay, projectionDisplay, projectionSelection);
- }
- else
- {
- IJ.log( " This image has to be a z-stack ! " );
- }
-
- }
-
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/jzy3D/OSDisplay.java b/src/main/java/fr/pasteur/ida/zellige/jzy3D/OSDisplay.java
index 0c2152b73eca3a27115cc60d9ebec7efb7a58830..b1d8a7ba26d9de079fa5d2a922bb9fcc26bd26e7 100644
--- a/src/main/java/fr/pasteur/ida/zellige/jzy3D/OSDisplay.java
+++ b/src/main/java/fr/pasteur/ida/zellige/jzy3D/OSDisplay.java
@@ -1,8 +1,8 @@
package fr.pasteur.ida.zellige.jzy3D;
import fr.pasteur.ida.zellige.surfaceConstruction.element.Coordinate;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSE;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSList;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ose.OSE;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ose.OSEList;
import org.jzy3d.analysis.AbstractAnalysis;
import org.jzy3d.chart.factories.AWTChartComponentFactory;
import org.jzy3d.colors.Color;
@@ -15,18 +15,18 @@ import java.util.Random;
public class OSDisplay extends AbstractAnalysis {
- private final OSList[] osLists;
+ private final OSEList[] oseLists;
- public OSDisplay(OSList[] osLists) {
- this.osLists = osLists;
+ public OSDisplay( OSEList[] oseLists ) {
+ this.oseLists = oseLists;
init();
}
public void init() {
int count = 0;
- for (OSList osList : osLists) {
- for ( OSE os : osList) {
+ for ( OSEList oseList : oseLists ) {
+ for ( OSE os : oseList ) {
count = count+os.size();
}
}
@@ -40,9 +40,9 @@ public class OSDisplay extends AbstractAnalysis {
float z;
int index = 0;
- for (OSList osList : osLists) {
+ for ( OSEList oseList : oseLists ) {
- for ( OSE os : osList) {
+ for ( OSE os : oseList ) {
// one color per OS
float G = r.nextFloat() ;
float R = r.nextFloat() ;
diff --git a/src/main/java/fr/pasteur/ida/zellige/jzy3D/ScatterDemo.java b/src/main/java/fr/pasteur/ida/zellige/jzy3D/ScatterDemo.java
deleted file mode 100644
index 7ef37fdf2137b4c858c92489ea36b14ec52d9c18..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/jzy3D/ScatterDemo.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package fr.pasteur.ida.zellige.jzy3D;
-
-
-public class ScatterDemo
-{//extends AbstractAnalysis{
-// public static void main(String[] args) throws Exception {
-// AnalysisLauncher.open(new ScatterDemo());
-// }
-
-// private ArrayList< Coordinate > maximumCoordinates;
-//
-// public ScatterDemo( ArrayList< Coordinate > coordinates )
-// {
-// this.maximumCoordinates = coordinates;
-// init();
-// }
-//
-// @Override
-// public void init()
-// {
-// if ( maximumCoordinates != null )
-// {
-// int size = 500000;
-// float a;
-//
-// Coord3d[] points = new Coord3d[maximumCoordinates.size()];
-// Color[] colors = new Color[maximumCoordinates.size()];
-// Coordinate c = null;
-//
-//// Random r = new Random();
-//// r.setSeed(0);
-//
-// int x;
-// int y;
-// int z;
-//
-// for ( int i = 0; i <= this.maximumCoordinates.size() - 1; i++ )
-// {
-// c = maximumCoordinates.get( i );
-// x = c.getX();
-// y = c.getY();
-// z = c.getZ();
-// points[i] = new Coord3d( x, y, z );
-// a = 2f;
-// colors[i] = new Color( 0, 0, 0, a );
-// System.out.println( points[i] );
-// }
-//
-// Scatter scatter = new Scatter( points, colors );
-// chart = AWTChartComponentFactory.chart( Quality.Advanced, "newt" );
-// chart.getScene().add( scatter );
-// }
-// }
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/jzy3D/ScatterDemo2.java b/src/main/java/fr/pasteur/ida/zellige/jzy3D/ScatterDemo2.java
deleted file mode 100644
index f909aaa44f7b9349a56fbcfd750d3aeff876f1bc..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/jzy3D/ScatterDemo2.java
+++ /dev/null
@@ -1,50 +0,0 @@
-package fr.pasteur.ida.zellige.jzy3D;
-
-import org.jzy3d.analysis.AbstractAnalysis;
-import org.jzy3d.analysis.AnalysisLauncher;
-import org.jzy3d.chart.factories.AWTChartComponentFactory;
-import org.jzy3d.colors.Color;
-import org.jzy3d.maths.Coord3d;
-import org.jzy3d.plot3d.primitives.Scatter;
-import org.jzy3d.plot3d.rendering.canvas.Quality;
-
-import java.util.Random;
-// comment for nothing
-
-public class ScatterDemo2 extends AbstractAnalysis
-{
- public static void main( String[] args ) throws Exception
- {
- AnalysisLauncher.open( new ScatterDemo2() );
- }
-
- @Override
- public void init( )
- {
- int size = 500000;
- float x;
- float y;
- float z;
- float a;
-
- Coord3d[] points = new Coord3d[ size ];
- Color[] colors = new Color[ size ];
-
- Random r = new Random();
- r.setSeed( 0 );
-
- for ( int i = 0; i < size; i++ )
- {
- x = r.nextFloat() - 0.5f;
- y = r.nextFloat() - 0.5f;
- z = r.nextFloat() - 0.5f;
- points[ i ] = new Coord3d( x, y, z );
- a = 0.25f;
- colors[ i ] = new Color( x, y, z, a );
- }
-
- Scatter scatter = new Scatter( points, colors );
- chart = AWTChartComponentFactory.chart( Quality.Advanced, "newt" );
- chart.getScene().add( scatter );
- }
-}
\ No newline at end of file
diff --git a/src/main/java/fr/pasteur/ida/zellige/jzy3D/ScatterDemo6.java b/src/main/java/fr/pasteur/ida/zellige/jzy3D/ScatterDemo6.java
deleted file mode 100644
index 58384f1668c67f7cb5fc0c483a786377e4e18c34..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/jzy3D/ScatterDemo6.java
+++ /dev/null
@@ -1,65 +0,0 @@
-package fr.pasteur.ida.zellige.jzy3D;
-
-
-import org.jzy3d.analysis.AbstractAnalysis;
-
-
-public class ScatterDemo6 extends AbstractAnalysis
-{
-
-
-// private AllSurface allSurface;
-//
-// public ScatterDemo6( AllSurface allSurface )
-// {
-// this.allSurface = allSurface;
-// }
-
- @Override
- public void init( )
- {
-// int size = allSurface.count();
-// System.out.println("final fr.pasteur.ida.zellige.surface number " + allSurface.getSurfaces().size());
-// System.out.println( Coordinate.number);
-// System.out.println( Surface1D.SurfaceCoordinates.ovsCount);
-// Coord3d[] points = new Coord3d[size];
-// Color[] colors = new Color[size];
-// int j = 0;
-// for(int i = 0; i <= allSurface.getSurfaces().size()-1; i++)
-//
-// {
-// Surface1D.SurfaceCoordinates coordinates = allSurface.getSurfaces().get( i );
-// Random r = new Random();
-// r.setSeed( i+3 );
-// float G = r.nextFloat();
-// float R = r.nextFloat();
-//
-// float B = r.nextFloat();
-// for ( OVSCoordinates ovsCoordinates : coordinates.getOvsCoordinates() )
-// {
-// Coordinate c = ovsCoordinates.getFist();
-// int x;
-// int y;
-// int z;
-//
-// while ( c != null )
-// {
-// x = c.getX();
-// y = c.getY();
-// z = c.getZ();
-//
-// points[j] = new Coord3d( x, y, z );
-// colors[j] = new Color( R, G, B, 5f );
-// c = c.getRight();
-// j++;
-// }
-// }
-// }
-// Scatter scatter = new Scatter( points, colors );
-// scatter.setWidth( 5 );
-// chart = AWTChartComponentFactory.chart( Quality.Advanced, "newt" );
-// chart.getScene().add( scatter );
-
- }
-}
-
diff --git a/src/main/java/fr/pasteur/ida/zellige/jzy3D/SurfaceDisplay.java b/src/main/java/fr/pasteur/ida/zellige/jzy3D/SurfaceDisplay.java
index c26cdcd0be19db68812e19aa709cdcfa43caeb0c..641b78de5702bf07a6fba08d26180040321420f6 100644
--- a/src/main/java/fr/pasteur/ida/zellige/jzy3D/SurfaceDisplay.java
+++ b/src/main/java/fr/pasteur/ida/zellige/jzy3D/SurfaceDisplay.java
@@ -14,7 +14,7 @@ import org.jzy3d.plot3d.rendering.canvas.Quality;
public class SurfaceDisplay extends AbstractAnalysis
{
- private Surface surface;
+ private final Surface surface;
public SurfaceDisplay( Surface surface )
{
@@ -36,7 +36,7 @@ public class SurfaceDisplay extends AbstractAnalysis
int z;
int index = 0;
int size = 0;
- for ( int i = 0; i <= surface.getLength() - 1; i++ )
+ for ( int i = 0; i <= surface.getHeight() - 1; i++ )
{
SurfaceLine surfaceLine = this.surface.get( i );
if ( surfaceLine != null )
diff --git a/src/main/java/fr/pasteur/ida/zellige/main/Main.java b/src/main/java/fr/pasteur/ida/zellige/main/Main.java
index f014ae61912712e9f1ce429887bdc6982da94899..0be1b5d25c4afe8e372632f074828b6f5cbc9675 100644
--- a/src/main/java/fr/pasteur/ida/zellige/main/Main.java
+++ b/src/main/java/fr/pasteur/ida/zellige/main/Main.java
@@ -1,23 +1,17 @@
package fr.pasteur.ida.zellige.main;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
+import fr.pasteur.ida.zellige.surfaceConstruction.parameters.AdvancedUserParameters;
+import fr.pasteur.ida.zellige.surfaceConstruction.construction.ReferenceSurfaceExtraction;
+import fr.pasteur.ida.zellige.surfaceConstruction.parameters.UserParameters;
import fr.pasteur.ida.zellige.utils.TestMIP;
import ij.IJ;
import ij.ImageJ;
-import io.scif.config.SCIFIOConfig;
import io.scif.img.IO;
import io.scif.img.SCIFIOImgPlus;
-import net.imagej.ImgPlus;
-import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
-import net.imglib2.img.ImgFactory;
-import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.img.display.imagej.ImageJFunctions;
-import net.imglib2.script.slice.SliceYZ;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
-import fr.pasteur.ida.zellige.surfaceConstruction.construction.SurfacesExtraction;
-import net.imglib2.type.numeric.real.FloatType;
/**
@@ -63,9 +57,9 @@ public class Main
// Input of the image.
final String imagePath =
-// "doc/STK_060.tif";
+ "doc/STK.tif";
// "C:\\Users\\ctrebeau\\Desktop\\MoucheAile\\STK\\STK_Mouche_c01_f0001_p005.tif";
- "C:\\Users\\ctrebeau\\Downloads\\phantom3b_combined.tif";
+// "C:\\Users\\ctrebeau\\Downloads\\phantom3b_combined.tif";
// "C:\\Users\\ctrebeau\\Desktop\\HighRes\\STK_170706_Vangl2-Lp-wt_E14.5_Phall_cochlea_01bHighRes_c01_f0001_p005.tif";
System.out.println(imagePath);
// Creation of the image : version with unsigned type. */
@@ -95,15 +89,17 @@ public class Main
System.out.println( System.lineSeparator() );
/* End of Print parameters.*/
+ UserParameters userParameters = new UserParameters( amplitude, otsu, sigmas, delta, "MIP" );
+ AdvancedUserParameters advancedUserParameters = new AdvancedUserParameters( k1, percent1, k2, percent2 );
IJ.log("Type: "+ imgPlus.firstElement().getClass().toGenericString());
if ( stackImage.numDimensions() == 3 )// Is it a stack ?
{
ImageJFunctions.show( stackImage, "original" );
ImageJFunctions.show( TestMIP.findMIP( stackImage, stackImage.factory() ), "MIP" );
-
- SurfacesExtraction.extract(stackImage, stackImage.factory(),amplitude,otsu, sigmas, false, delta, false,
- false, true, "MIP", k1, percent1, k2, percent2);
+ ReferenceSurfaceExtraction rse = new ReferenceSurfaceExtraction<>( stackImage, stackImage.factory(),userParameters, advancedUserParameters );
+ rse.extract();
+ rse.project();
}
else
{
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/OSConstruction.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/OSConstruction.java
deleted file mode 100644
index df468e813fadf5af7ca6305e5147d503f4b18d4c..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/OSConstruction.java
+++ /dev/null
@@ -1,244 +0,0 @@
-package fr.pasteur.ida.zellige.surfaceConstruction.construction;
-
-import fr.pasteur.ida.zellige.surfaceConstruction.element.Coordinate;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSE;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSEStartingStatus;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSList;
-
-import java.util.ArrayList;
-import java.util.LinkedList;
-import java.util.Queue;
-import java.util.TreeMap;
-
-
-/**
- * This class contains a main static method for the construction of OS : {@code findOS}.
- */
-public class OSConstruction
-{
-
- /**
- * This method finds all the possible 2D surfaces that can be created from the coordinates detected as
- * local maximums on a array of {@link }.
- *
- * @param rawCoordinates - the raw Coordinates from the projection.
- * @return all the orthogonal surfaces for the projection as an {@link ArrayList< OSE >}.
- */
- public static OSList findOS( Pixels[] rawCoordinates, int dimension , OSEStartingStatus startingStatus)
- {
- if ( dimension == 1 )
- {
- reset( rawCoordinates );// the number of right and left coordinates are reset to 0.
- }
- ArrayList < Coordinate > startingCoordinates = checkForSideCoordinates( rawCoordinates );
- OSList paths = findSimplePaths( startingCoordinates, rawCoordinates, dimension, startingStatus );
- OSList finalPaths = findComplexPaths( paths, dimension );
- if ( dimension == 0 )
- {
- finalPaths.removeIf( os -> os.size() < 3 );// shortest ones are removed
- }
- for ( OSE os : finalPaths )
- {
- os.set(dimension);
- }
- finalPaths.reset();
- return finalPaths;
- }
-
- private static OSList findSimplePaths (ArrayList< Coordinate> startingCoordinates, Pixels[] rawCoordinates,
- int dimension, OSEStartingStatus occurrence)
- {
- Queue < Coordinate > firstQueue = new LinkedList <>( startingCoordinates );// Add the coordinates with no left coordinates in
- // the queue
- OSList smallPath = new OSList();
- while ( !firstQueue.isEmpty() )
- {
- Coordinate current = firstQueue.remove();
- OSE os = new OSE(occurrence);
- os.add( current );
- findSimplePaths( rawCoordinates, smallPath, os, current, dimension, firstQueue );
- }
- return smallPath;
- }
-
- /**
- * @param rawCoordinates - the raw Coordinates from the projection.
- * @param smallPath - the one-Z-OS
- * @param os - the first OS considered.
- * @param current - the starting {@link Coordinate} considered.
- * @param dimension - the dimension of the OS construction.
- */
- private static void findSimplePaths
- ( Pixels[] rawCoordinates,
- ArrayList < OSE > smallPath, OSE os, Coordinate current, int dimension, Queue < Coordinate > queue )
- {
- int i;
- if ( dimension == 0 )
- {
- i = current.getX();
- }
- else
- {
- i = current.getY();
- }
- while ( i <= rawCoordinates.length - 2 // x must be < to the length of the image minus 1 because [X + 1]
- && rawCoordinates[ i ] != null // the contents in the array at index x must not be null
- && rawCoordinates[ i + 1 ] != null // the contents in the array at index (x +1) must not be null
- && current!= null )
- {
- Coordinate next = current.getNext( rawCoordinates[ i + 1 ], 0 );
- if ( next != null )// Conditions : |x1 - x2 |= 1 => only 1D surface
- {
- os.add( next );
- }
- else
- {
- if ( ( i ) < rawCoordinates.length - 3
- && rawCoordinates[ i + 2 ] != null// the contents in the array at index (x +1) must not
- // be null
- && current.getRightNumber() == 0 )
- {
- next = current.getNext( rawCoordinates[ i + 2 ], 0 );
- if ( next != null )//fake coordinate
- {
- if ( dimension == 0 )
- {
- os.add( new Coordinate(current.getX() + 1, current.getY(), current.getZ() ) );
- }
- else
- {
- os.add( new Coordinate( current.getX(), current.getY() + 1, current.getZ() ) );
- }
- os.add( next );
- queue.remove( next );
- i++;
- }
- }
- }
- current = next;
- i++; //increment of the index
- }
- smallPath.add( os );
- }
-
- /**
- * @param shortPaths - the list of one-z-OS.
- * @param dimension - the dimension considered.
- * @return - the list of "big paths" OS.
- */
- private static OSList findComplexPaths( OSList shortPaths, int dimension )
- {
- OSList paths = new OSList();
- Queue < OSE > queue = new LinkedList <>( shortPaths );
- while ( !queue.isEmpty() )
- {
- OSE first = queue.remove();
- shortPaths.remove( first );
- findComplexPaths( first, shortPaths, queue, paths, dimension );
- }
- return paths;
- }
-
- /**
- * @param first - the starting OS.
- * @param smallPaths - the list of all small path OS.
- * @param queue - the remaining OS.
- * @param longPaths - the list of long path OS.
- * @param dimension - the dimension considered.
- */
- private static void findComplexPaths( OSE first,
- ArrayList < OSE > smallPaths,
- Queue < OSE > queue, ArrayList < OSE > longPaths, int dimension )
- {
- for ( OSE o : smallPaths )
- {
- if ( first.isNextTo( o, dimension ) )
- {
- first.addAll( o );
- o.setVisited( true );
- queue.remove( o );
- }
- }
- smallPaths.removeIf( OSE::isVisited );
- longPaths.add( first );
- }
-
- /**
- * Stores the coordinates that don't have a coordinate to the left.
- *
- * @param slice - a one-dimensional array containing the local maximums.
- * @return - a list of coordinates that don't have a coordinate to the left.
- */
- private static ArrayList < Coordinate > checkForSideCoordinates( Pixels[] slice )
- {
- /* Stores the coordinates that have no coordinates to the left.*/
- ArrayList < Coordinate > noLeftCoordinates = new ArrayList <>();
- /* Starting point. */
- int start = 0;
- while ( start <= slice.length - 3 && slice[ start ] == null )
- {
- start++;//the index starts where a List of Coordinates is found in the array
- }
- if ( slice[ start ] != null && slice[ start + 1 ] != null ) //some Coordinates were found
- {
- /* For the first list of coordinates. */
- for ( int i = 0; i <= slice[ start ].size() - 1; i++ )// the first coordinates of the array have obviously no left coordinates
- {
- Coordinate coordinate = slice[ start ].get( i );
- noLeftCoordinates.add( coordinate );
- coordinate.setRightCoordinates( slice[ start + 1 ] );
- }
- }
- /* For the rest. */
- for ( int i = start + 1; i <= slice.length - 2; i++ )
- {
- if ( slice[ i ] != null )
- {
- for ( Coordinate coordinate : slice[ i ].get() )
- {
- coordinate.setRightCoordinates( slice[ i + 1 ] );
- coordinate.setLeftCoordinates( slice[ i - 1 ] );
- boolean hasNoLeft = coordinate.numberOfNeighbours( slice[ i - 1 ], 0 )== 0;
- if ( hasNoLeft )
- {
- noLeftCoordinates.add( coordinate );
- }
- }
- }
- }
- /* the last one */ //Avoid ArrayOutOfBoundException
- int end = slice.length - 1;
- if ( slice[ end ] != null && slice[ end - 1 ] != null )
- {
- for ( Coordinate coordinate : slice[ end ].get() )
- {
- coordinate.setLeftCoordinates( slice[ end - 1 ] );
- boolean hasNoLeft = coordinate.numberOfNeighbours( slice[ end - 1 ], 0 )== 0;
- if ( hasNoLeft )
- {
- noLeftCoordinates.add( coordinate );
- }
- }
- }
- return noLeftCoordinates;
- }
-
- /**
- * Resets the parameters of each {@link Coordinate } for a given {@link Pixels} array
- * before the Y dimension reconstruction ( rightsNumber , leftsNumber, noLeft, queue ).
- *
- * @param slice - the {@link Pixels} array considered.
- */
- private static void reset( Pixels[] slice )
- {
- for ( Pixels pixels : slice )
- {
- if ( pixels != null )
- {
- pixels.resetSideCoordinate();
- }
- }
- }
-}
-
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/OSEListConstruction.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/OSEListConstruction.java
new file mode 100644
index 0000000000000000000000000000000000000000..2b573922e769630c45f3880564aa02fce662197a
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/OSEListConstruction.java
@@ -0,0 +1,272 @@
+package fr.pasteur.ida.zellige.surfaceConstruction.construction;
+
+import fr.pasteur.ida.zellige.surfaceConstruction.element.Coordinate;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ose.OSE;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ose.OSEList;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ose.OSEStartingStatus;
+
+import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.Queue;
+
+
+/**
+ * This class contains a main method for the construction of OSE : {@code findOS}.
+ */
+public class OSEListConstruction
+{
+ private final Pixels[][] maximums;
+ private final OSEList[] oseLists;
+ private final OSEStartingStatus startingStatus;
+ private final int dimension;
+
+ public OSEListConstruction( Pixels[][] maximums , int dimension)
+ {
+ this.maximums = maximums;
+ this.oseLists = new OSEList[maximums.length];
+ this.dimension = dimension;
+ this.startingStatus = new OSEStartingStatus( dimension );
+ }
+
+ public void run()
+ {
+ for ( int i = 0; i <= maximums.length - 1; i++ )
+ {
+ oseLists[ i ] = findOSE( maximums[ i ] );
+ }
+ startingStatus.setStartingStatus();
+ System.out.println( "Starting size = " + startingStatus.getMinimumSize());
+ }
+
+ /**
+ * This method finds all the possible 2D surfaces that can be created from the coordinates detected as
+ * local maximums on a array of {@link }.
+ *
+ * @param rawCoordinates - the raw Coordinates from the projection.
+ * @return all the orthogonal surfaces for the projection as an {@link ArrayList<OSE>}.
+ */
+ private OSEList findOSE( Pixels[] rawCoordinates )
+ {
+ if ( dimension == 1 )
+ {
+ reset( rawCoordinates );// the number of right and left coordinates are reset to 0.
+ }
+ ArrayList< Coordinate > startingCoordinates = checkForSideCoordinates( rawCoordinates );
+ OSEList paths = findSimplePaths( startingCoordinates, rawCoordinates );
+ OSEList finalPaths = findComplexPaths( paths );
+ if ( dimension == 0 )
+ {
+ finalPaths.removeIf( ose -> ose.size() < 3 );// shortest ones are removed
+ }
+ for ( OSE ose : finalPaths )
+ {
+ ose.set();
+ }
+ finalPaths.reset();
+ return finalPaths;
+ }
+
+ private OSEList findSimplePaths( ArrayList< Coordinate > startingCoordinates, Pixels[] rawCoordinates )
+ {
+ Queue< Coordinate > firstQueue = new LinkedList<>( startingCoordinates );// Add the coordinates with no left coordinates in
+ // the queue
+ OSEList smallPath = new OSEList();
+ while ( ! firstQueue.isEmpty() )
+ {
+ Coordinate current = firstQueue.remove();
+ OSE ose = new OSE( startingStatus );
+ ose.add( current );
+ findSimplePaths( rawCoordinates, smallPath, ose, current, firstQueue );
+ }
+ return smallPath;
+ }
+
+ /**
+ * @param rawCoordinates - the raw Coordinates from the projection.
+ * @param smallPath - the one-Z-OSE
+ * @param ose - the first OSE considered.
+ * @param current - the starting {@link Coordinate} considered.
+ */
+ private void findSimplePaths
+ ( Pixels[] rawCoordinates,
+ ArrayList< OSE > smallPath, OSE ose, Coordinate current, Queue< Coordinate > queue )
+ {
+ int i;
+ if ( dimension == 0 )
+ {
+ i = current.getX();
+ }
+ else
+ {
+ i = current.getY();
+ }
+ while ( i <= rawCoordinates.length - 2 // x must be < to the length of the image minus 1 because [X + 1]
+ && rawCoordinates[ i ] != null // the contents in the array at index x must not be null
+ && rawCoordinates[ i + 1 ] != null // the contents in the array at index (x +1) must not be null
+ && current != null )
+ {
+ Coordinate next = current.getNext( rawCoordinates[ i + 1 ], 0 );
+ if ( next != null )// Conditions : |x1 - x2 |= 1 => only 1D surface
+ {
+ ose.add( next );
+ }
+ else
+ {
+ if ( ( i ) < rawCoordinates.length - 3
+ && rawCoordinates[ i + 2 ] != null// the contents in the array at index (x +1) must not
+ // be null
+ && current.getRightNumber() == 0 )
+ {
+ next = current.getNext( rawCoordinates[ i + 2 ], 0 );
+ if ( next != null )//fake coordinate
+ {
+ if ( dimension == 0 )
+ {
+ ose.add( new Coordinate( current.getX() + 1, current.getY(), current.getZ() ) );
+ }
+ else
+ {
+ ose.add( new Coordinate( current.getX(), current.getY() + 1, current.getZ() ) );
+ }
+ ose.add( next );
+ queue.remove( next );
+ i++;
+ }
+ }
+ }
+ current = next;
+ i++; //increment of the index
+ }
+ smallPath.add( ose );
+ }
+
+ /**
+ * @param shortPaths - the list of one-z-OSE.
+ * @return - the list of "big paths" OSE.
+ */
+ private OSEList findComplexPaths( OSEList shortPaths )
+ {
+ OSEList paths = new OSEList();
+ Queue< OSE > queue = new LinkedList<>( shortPaths );
+ while ( ! queue.isEmpty() )
+ {
+ OSE first = queue.remove();
+ shortPaths.remove( first );
+ findComplexPaths( first, shortPaths, queue, paths );
+ }
+ return paths;
+ }
+
+ /**
+ * @param first - the starting OSE.
+ * @param smallPaths - the list of all small path OSE.
+ * @param queue - the remaining OSE.
+ * @param longPaths - the list of long path OSE.
+ */
+ private void findComplexPaths( OSE first,
+ ArrayList< OSE > smallPaths,
+ Queue< OSE > queue, ArrayList< OSE > longPaths )
+ {
+ for ( OSE o : smallPaths )
+ {
+ if ( first.isNextTo( o, dimension ) )
+ {
+ first.addAll( o );
+ o.setVisited( true );
+ queue.remove( o );
+ }
+ }
+ smallPaths.removeIf( OSE::isVisited );
+ longPaths.add( first );
+ }
+
+ /**
+ * Stores the coordinates that don't have a coordinate to the left.
+ *
+ * @param slice - a one-dimensional array containing the local maximums.
+ * @return - a list of coordinates that don't have a coordinate to the left.
+ */
+ private ArrayList< Coordinate > checkForSideCoordinates( Pixels[] slice )
+ {
+ /* Stores the coordinates that have no coordinates to the left.*/
+ ArrayList< Coordinate > noLeftCoordinates = new ArrayList<>();
+ /* Starting point. */
+ int start = 0;
+ while ( start <= slice.length - 3 && slice[ start ] == null )
+ {
+ start++;//the index starts where a List of Coordinates is found in the array
+ }
+ if ( slice[ start ] != null && slice[ start + 1 ] != null ) //some Coordinates were found
+ {
+ /* For the first list of coordinates. */
+ for ( int i = 0; i <= slice[ start ].size() - 1; i++ )// the first coordinates of the array have obviously no left coordinates
+ {
+ Coordinate coordinate = slice[ start ].get( i );
+ noLeftCoordinates.add( coordinate );
+ coordinate.setRightCoordinates( slice[ start + 1 ] );
+ }
+ }
+ /* For the rest. */
+ for ( int i = start + 1; i <= slice.length - 2; i++ )
+ {
+ if ( slice[ i ] != null )
+ {
+ for ( Coordinate coordinate : slice[ i ].get() )
+ {
+ coordinate.setRightCoordinates( slice[ i + 1 ] );
+ coordinate.setLeftCoordinates( slice[ i - 1 ] );
+ boolean hasNoLeft = coordinate.numberOfNeighbours( slice[ i - 1 ], 0 ) == 0;
+ if ( hasNoLeft )
+ {
+ noLeftCoordinates.add( coordinate );
+ }
+ }
+ }
+ }
+ /* the last one */ //Avoid ArrayOutOfBoundException
+ int end = slice.length - 1;
+ if ( slice[ end ] != null && slice[ end - 1 ] != null )
+ {
+ for ( Coordinate coordinate : slice[ end ].get() )
+ {
+ coordinate.setLeftCoordinates( slice[ end - 1 ] );
+ boolean hasNoLeft = coordinate.numberOfNeighbours( slice[ end - 1 ], 0 ) == 0;
+ if ( hasNoLeft )
+ {
+ noLeftCoordinates.add( coordinate );
+ }
+ }
+ }
+ return noLeftCoordinates;
+ }
+
+ /**
+ * Resets the parameters of each {@link Coordinate } for a given {@link Pixels} array
+ * before the Y dimension reconstruction ( rightsNumber , leftsNumber, noLeft, queue ).
+ *
+ * @param slice - the {@link Pixels} array considered.
+ */
+ private void reset( Pixels[] slice )
+ {
+ for ( Pixels pixels : slice )
+ {
+ if ( pixels != null )
+ {
+ pixels.resetSideCoordinate();
+ }
+ }
+ }
+
+
+ public OSEList[] getOseLists()
+ {
+ return oseLists;
+ }
+
+ public OSEStartingStatus getStartingStatus()
+ {
+ return startingStatus;
+ }
+}
+
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/ReferenceSurfaceExtraction.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/ReferenceSurfaceExtraction.java
new file mode 100644
index 0000000000000000000000000000000000000000..3bd58de8119623e4ad034cd4a17295ae0c9cc090
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/ReferenceSurfaceExtraction.java
@@ -0,0 +1,294 @@
+package fr.pasteur.ida.zellige.surfaceConstruction.construction;
+
+import fr.pasteur.ida.zellige.surfaceConstruction.parameters.AdvancedUserParameters;
+import fr.pasteur.ida.zellige.surfaceConstruction.parameters.DisplayParameter;
+import fr.pasteur.ida.zellige.exception.FirstRoundConstructionException;
+import fr.pasteur.ida.zellige.exception.NoSurfaceFoundException;
+import fr.pasteur.ida.zellige.jzy3D.LocalMaximumsDisplay;
+import fr.pasteur.ida.zellige.jzy3D.OSDisplay;
+import fr.pasteur.ida.zellige.jzy3D.SurfaceDisplay;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ReferenceSurface;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.Surface;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ose.OSEList;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.surfaceLine.SurfaceLine;
+import fr.pasteur.ida.zellige.surfaceConstruction.parameters.UserParameters;
+import fr.pasteur.ida.zellige.utils.*;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.img.Img;
+import net.imglib2.img.ImgFactory;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
+import org.jzy3d.analysis.AnalysisLauncher;
+
+import java.util.ArrayList;
+
+
+
+public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T > >
+{
+
+ private final ArrayList< ReferenceSurface <T>> referenceSurfaces = new ArrayList<>();
+ private final RandomAccessibleInterval< T > input;
+ private final ImgFactory<T> factory;
+ private final UserParameters userParameters;
+ private final AdvancedUserParameters advancedUserParameters;
+ public ReferenceSurfaceExtraction( RandomAccessibleInterval< T > input, ImgFactory<T> factory,
+ UserParameters userParameters, AdvancedUserParameters advancedUserParameters)
+ {
+ this.input = input;
+ this.factory = factory;
+ this.userParameters = userParameters;
+ this.advancedUserParameters = advancedUserParameters;
+ }
+
+
+ public void extract( )
+ {
+ /* First step : Pixel selection */
+ SurfacePixelSelection selection = new SurfacePixelSelection( userParameters );
+ selection.run( input );
+ Pixels[][] maximums = selection.getMaximums();
+ /* Second step : Surface construction in 2 rounds */
+ try
+ {
+ /* First round construction*/
+ double percent1 = advancedUserParameters.getPercent1();
+ int k1 = advancedUserParameters.getK1();
+ ArrayList< Surface > tempSurfaces = firstRoundConstruction( maximums, percent1, k1);
+ System.out.println( "first round surfaces = " + tempSurfaces.size() );
+
+ /* Second round construction */
+ double percent2 = advancedUserParameters.getPercent2();
+ int k2 = advancedUserParameters.getK2();
+ ArrayList< Surface > finalSurfaces = secondRoundConstruction( tempSurfaces, percent2, k2 );
+ System.out.println( "second round surfaces = " + finalSurfaces.size() );
+
+ /* Process of zMaps */
+ processZMap( finalSurfaces );
+
+ System.out.println( "The end" );
+ }
+ catch ( Exception e )
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /* ----- First and second round construction methods. ----- */
+ private ArrayList< Surface > firstRoundConstruction( Pixels[][] maximums, double percent, int k ) throws NoSurfaceFoundException
+ {
+ int dimension = 0;
+ ArrayList<Surface> surfaces = constructSurfaces( maximums, dimension, percent, k );
+ if ( ! surfaces.isEmpty() )
+ {
+ mergeReferenceSurface( surfaces );
+ }
+ else
+ {
+ System.out.println( "No Surface Exception" );
+ throw new FirstRoundConstructionException();
+ }
+ return surfaces;
+ }
+
+ /**
+ * Rebuilds the double pixel array from the {@link SurfaceLine} array
+ * of a {@link Surface} for a construction in the height dimension.
+ *
+ * @param surface - the {@link SurfaceLine} array of a {@link Surface}
+ * @return a {@link Surface} specific double pixel array.
+ */
+ private Pixels[][] rebuildPixelsArray( Surface surface )
+ {
+ int width = surface.get().length;
+ int height = surface.get()[0].getLength();
+ Pixels[][] tempCoordinates = new Pixels[ height ][ width ]; // Transposed array
+ for ( int i = 0; i <= width - 1; i++ )
+ {
+ for ( int j = 0; j <= height - 1; j++ )
+ {
+ if ( surface.get( i ) != null )
+ {
+ tempCoordinates[ j ][ i ] = surface.get( i ).get( j );
+ }
+ }
+ }
+ displayMaximums( tempCoordinates );
+ return tempCoordinates;
+ }
+
+ /**
+ * Reconstructs the TempSurface objects of the specified list in dimension width.
+ *
+ * @param surfaces - the list of TempSurface objects.
+ */
+ private ArrayList< Surface > secondRoundConstruction( ArrayList< Surface > surfaces, double percent, int k ) throws NoSurfaceFoundException
+ {
+ int dimension = 1;
+ ArrayList< Surface > finalSurfaces = new ArrayList<>();
+ System.out.println( "========================================" );
+ for ( Surface surface : surfaces )
+ {
+ int width = surface.getHeight();
+ if ( surface.hasDuplicate() )// CoordinateList instead of Coordinate
+ {
+ Pixels[][] maximums = rebuildPixelsArray( surface );
+ ArrayList< Surface > temps = constructSurfaces( maximums,dimension, percent, k);
+ if ( temps.isEmpty() )
+ {
+ System.out.println( "small surface in second round" );
+// throw new SecondRoundConstructionException();
+ }
+ else
+ {
+ finalSurfaces.addAll( temps );
+ }
+ }
+ else
+ {
+ finalSurfaces.add( surface.transpose(width) );
+ }
+ }
+ mergeReferenceSurface( surfaces);
+ return finalSurfaces;
+
+ }
+
+ private Img<UnsignedShortType> processedZMap(Surface surface)
+ {
+ // First step : fill in the holes with linear interpolation. */
+ Img< UnsignedShortType > interpolated = Interpolation.run( surface.getZMap() );
+ Img< UnsignedShortType > smoothed = interpolated.copy();
+ ImageJFunctions.show( smoothed, "smoothed" );
+ // Second step: smooth the elevation map with gaussian blur
+ Utils.gaussConvolution( interpolated, smoothed, new double[]{ 1.0, 1.0 } );
+ return smoothed;
+ }
+
+ //TODO Handle the NOSurfaceFoundException dynamically : this particular surface has to be constructed with a
+ // smaller StartingOSMinimumSize but not necessary the other ones.
+ // May be add a static variable to store the maximum OS size per surfaces
+ //
+
+ /**
+ * Merges the TempSurface objects of the specified list.
+ *
+ * @param surfaces - the list to merge
+ */
+ private void mergeReferenceSurface( ArrayList< Surface > surfaces )
+ {
+ // Merging step.
+ ArrayList< Surface > toRemoved = new ArrayList<>();
+ for ( int i = surfaces.size() - 1; i > 0; i-- )
+ {
+ Surface one = surfaces.get( i );
+ for ( int j = i - 1; j >= 0; j-- )
+ {
+ Surface two = surfaces.get( j );
+ if ( one.sameSurface( two ) )
+ {
+ two.merge( one );
+ toRemoved.add( one );
+ }
+ }
+ }
+ surfaces.removeAll( toRemoved );
+ }
+
+ private OSEList[] constructOSLists( Pixels[][] maximums, int dimension)
+ {
+ OSEListConstruction construction = new OSEListConstruction( maximums, dimension );
+ construction.run();
+ return construction.getOseLists();
+ }
+
+
+ private ArrayList<Surface> constructSurfaces(Pixels[][] maximums, int dimension, double percent, int k)
+ {
+ int surfaceLineLength = maximums[0].length;
+ OSEList[] oseLists = constructOSLists( maximums, dimension );
+ SurfacesReconstruction surfacesReconstruction = new SurfacesReconstruction(dimension, oseLists,surfaceLineLength, percent, k);
+ surfacesReconstruction.buildSurfaces( );
+ System.out.println(" Small Surface count : " + surfacesReconstruction.getSmallSurfaceCount());
+ return surfacesReconstruction.getSurfaces();
+ }
+
+ private void processZMap(ArrayList<Surface> surfaces)
+ {
+ int index = 0;
+ for( Surface surface : surfaces )
+ {
+ displaySurface( surface );
+ Img< UnsignedShortType > processedZMap = processedZMap( surface );
+ ReferenceSurface< T > referenceSurface = new ReferenceSurface<>( input, factory, processedZMap, index++ );
+ referenceSurfaces.add( referenceSurface );
+ }
+ }
+
+ public void project()
+ {
+ for(ReferenceSurface<T> referenceSurface : referenceSurfaces)
+ {
+ referenceSurface.setProjection( userParameters.getProjectionType(), userParameters.getDelta() );
+ DisplayParameter displayParameter = new DisplayParameter( userParameters.getDelta(), true,
+ true, true, true );
+ referenceSurface.display( displayParameter );
+ }
+ }
+
+
+ /* ----- Displaying methods -----*/
+ /**
+ * Displays the local maximums found using jzy3D package.
+ */
+ public static void displayMaximums( Pixels[][] maximums )
+ {
+ try
+ {
+ LocalMaximumsDisplay localMaximumsDisplay = new LocalMaximumsDisplay( maximums );
+ AnalysisLauncher.open( localMaximumsDisplay );
+ }
+ catch ( Exception e )
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Displays the local maximums found using jzy3D package.
+ */
+ public static void displayOS( OSEList[] oseLists )
+ {
+ try
+ {
+ OSDisplay display = new OSDisplay( oseLists );
+ AnalysisLauncher.open( display );
+ }
+ catch ( Exception e )
+ {
+ e.printStackTrace();
+ }
+ }
+
+
+
+ public static void displaySurface( Surface surface )
+ {
+ try
+ {
+ SurfaceDisplay s = new SurfaceDisplay( surface );
+ AnalysisLauncher.open( s );
+ }
+ catch ( Exception e )
+ {
+ e.printStackTrace();
+ }
+
+ }
+
+}
+
+
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/SurfacePixelSelection.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacePixelSelection.java
similarity index 77%
rename from src/main/java/fr/pasteur/ida/zellige/utils/SurfacePixelSelection.java
rename to src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacePixelSelection.java
index 7691c3e86b9ba9d70b83c2bf3a844e38533da7aa..aa34c762171b31e780f748682c82a7d96833466b 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/SurfacePixelSelection.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacePixelSelection.java
@@ -1,12 +1,13 @@
-package fr.pasteur.ida.zellige.utils;
+package fr.pasteur.ida.zellige.surfaceConstruction.construction;
import fr.pasteur.ida.zellige.jzy3D.LocalMaximumsDisplay;
+import fr.pasteur.ida.zellige.surfaceConstruction.parameters.UserParameters;
import fr.pasteur.ida.zellige.surfaceConstruction.element.Coordinate;
import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
+import fr.pasteur.ida.zellige.utils.*;
import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.converter.Converters;
-import net.imglib2.converter.RealFloatConverter;
import net.imglib2.converter.readwrite.RealFloatSamplerConverter;
import net.imglib2.img.Img;
import net.imglib2.img.ImgFactory;
@@ -16,34 +17,36 @@ import net.imglib2.type.NativeType;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.real.FloatType;
-import net.imglib2.util.ImgUtil;
import org.jzy3d.analysis.AnalysisLauncher;
public class SurfacePixelSelection
{
+ private final UserParameters userParameters;
+ private Pixels[][] maximums;
+
+ public SurfacePixelSelection( UserParameters userParameters )
+ {
+ this.userParameters = userParameters;
+ }
/**
*
* @param source
- * @param amplitude
- * @param threshold
- * @param sigmas
* @param <T>
* @return
*/
- public static < T extends RealType< T > & NativeType< T > > Pixels[][] run( RandomAccessibleInterval< T > source, double amplitude, double threshold, int sigmas )
+ public < T extends RealType< T > & NativeType< T > > void run( RandomAccessibleInterval< T > source )
{
/* Pretreatment of the image.*/
Img< FloatType > normalized = pretreatment( source );
ImageJFunctions.show( normalized.copy(), "converted, blurred and normalized " );
ImgFactory<FloatType> factory = normalized.factory();
/* Local maximum search and selection */
- Pixels[][] maximums = maximumSearch( normalized, factory, amplitude,threshold, sigmas );
+ maximums = maximumSearch( normalized, factory );
/* Output */
displayMaximums( maximums );
- return maximums;
}
/**
@@ -52,7 +55,7 @@ public class SurfacePixelSelection
* @param <T>
* @return
*/
- private static < T extends RealType< T > & NativeType< T > >Img<FloatType> pretreatment( RandomAccessibleInterval< T > source )
+ private < T extends RealType< T > & NativeType< T > >Img<FloatType> pretreatment( RandomAccessibleInterval< T > source )
{
// Conversion into FloatType for the derivative computation (negative values)
RandomAccessibleInterval< FloatType > converted = Converters.convert( source, new RealFloatSamplerConverter< T >() );
@@ -65,44 +68,41 @@ public class SurfacePixelSelection
return Utils.normalizeImage( c, c.factory());
}
-
/**
*
* @param input
- * @param amplitude
- * @param threshold
- * @param sigma
+ * @param factory
* @param <T>
* @return
*/
- private static < T extends RealType< T > & NativeType< T > > Pixels[][] maximumSearch( RandomAccessibleInterval< T > input,ImgFactory<T> factory, double amplitude, double threshold, int sigma )
+ private < T extends RealType< T > & NativeType< T > > Pixels[][] maximumSearch( RandomAccessibleInterval< T > input,ImgFactory<T> factory )
{
/* Grid of amplitude thresholds */
- Img< FloatType > amplitudeImg = MaximumAmplitudeClassification.find(input,factory, amplitude, 0.10);
+ Img< FloatType > amplitudeImg = MaximumAmplitudeClassification.find(input,factory,userParameters.getAmplitude() , 0.10);
ImageJFunctions.show( amplitudeImg," amplitude" );
/* Grid of local thresholds*/
- Img< BitType > thresholds = LocalOtsuClassification.find( input, factory, threshold );
+ Img< BitType > thresholds = LocalOtsuClassification.find( input, factory, userParameters.getThreshold());
/* Pixel selection */
Img<FloatType> finalList = Threshold.classification( amplitudeImg, amplitudeImg.factory(), thresholds );
/* Dilatation of the resulting image*/
+ double sigma = userParameters.getSigmas();
Utils.gaussConvolution( finalList.copy(), finalList, new double[]{ sigma, sigma, 1 } );
ImageJFunctions.show(finalList, "blurred maximums" );
/* Local maximum detection due to previous smoothing*/
- finalList = LocalMaximumDetection.findMaximums( finalList.copy(), finalList.factory() );
+ finalList = LocalExtremaDetection.findMaxima( finalList.copy(), finalList.factory() );
return buildPixelArray( finalList );
}
-
/**
*
* @param stack
* @param <T>
* @return
*/
- public static < T extends RealType< T > & NativeType< T > > Pixels[][] buildPixelArray(
+ public < T extends RealType< T > & NativeType< T > > Pixels[][] buildPixelArray(
final RandomAccessibleInterval< T > stack )
{
RandomAccess< T > access = stack.randomAccess();
@@ -147,4 +147,8 @@ public class SurfacePixelSelection
}
}
+ public Pixels[][] getMaximums()
+ {
+ return maximums;
+ }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacesExtraction.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacesExtraction.java
deleted file mode 100644
index e62720161e0951a3b7ee6fe2f08fd8bd731dbf0b..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacesExtraction.java
+++ /dev/null
@@ -1,338 +0,0 @@
-package fr.pasteur.ida.zellige.surfaceConstruction.construction;
-
-import fr.pasteur.ida.zellige.exception.FirstRoundConstructionException;
-import fr.pasteur.ida.zellige.exception.NoSurfaceFoundException;
-import fr.pasteur.ida.zellige.jzy3D.LocalMaximumsDisplay;
-import fr.pasteur.ida.zellige.jzy3D.OSDisplay;
-import fr.pasteur.ida.zellige.jzy3D.SurfaceDisplay;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.Surface;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSE;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSEStartingStatus;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSList;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.surfaceLine.SurfaceLine;
-import fr.pasteur.ida.zellige.utils.*;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.img.Img;
-import net.imglib2.img.ImgFactory;
-import net.imglib2.img.display.imagej.ImageJFunctions;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.type.numeric.integer.UnsignedShortType;
-import org.jzy3d.analysis.AnalysisLauncher;
-
-import java.util.ArrayList;
-
-
-
-public class SurfacesExtraction
-{
-
- public static < T extends RealType< T > & NativeType< T > > void extract(
- RandomAccessibleInterval< T > input, ImgFactory<T> factory,double amplitude, double threshold, int sigmas,
- boolean zMapDisplay, int delta,
- boolean extractedStackDisplay,
- boolean heightMapDisplay,
- boolean projectionDisplay,
- String projectionType ,
- int k1, double percent1, int k2, double percent2)
- {
- /* First step : Pixel selection */
- Pixels[][] maximums = SurfacePixelSelection.run( input, amplitude, threshold, sigmas );
- int width = ( int ) input.dimension( 0 );
- int height = ( int ) input.dimension( 1 );
- try
- {
- /* First round construction*/
- ArrayList< Surface > surfaces = firstRoundConstruction( maximums, width, height , percent1, k1);
- System.out.println( "first round surfaces = " + surfaces.size() );
-//
- for (Surface surface : surfaces) {
- displaySurface(surface);
- }
- // Second round construction
- ArrayList< Surface > finalSurfaces = secondRoundConstruction( surfaces, width, height, percent2, k2 );
-// if ( !finalSurfaces.isEmpty() )
-// {
- int index = 0;
- for ( Surface surface : finalSurfaces )
- {
- System.out.println( "Surface number " + index );
-// displaySurface(surface);
- Img< UnsignedShortType > zMap = surface.getZMap();
- projection( input, factory,delta, zMap, zMapDisplay,
- extractedStackDisplay, heightMapDisplay,
- projectionDisplay, projectionType, index );
- index++;
- }
-
-// // Display the projection
- System.out.println( "The end" );
- }
- catch ( Exception e )
- {
- e.printStackTrace();
- }
- }
-
-
- /**
- * Creates the OS for each orthogonal section from the maximum coordinates found according to the dimension.
- *
- * @param maximums - the local maximums found with the {@link LocalMaximumDetection} class.
- * @param osListsArray - the OS corresponding to a 1D surface.
- */
- private static void set( Pixels[][] maximums, OSList[] osListsArray, int dimension, OSEStartingStatus startingStatus )
- {
-
-
- for ( int i = 0; i <= maximums.length - 1; i++ )
- {
- osListsArray[ i ] = OSConstruction.findOS( maximums[ i ], dimension, startingStatus );
- }
- startingStatus.setStartingStatus();
- }
-
- /* ----- First and second round construction methods. ----- */
- private static ArrayList< Surface > firstRoundConstruction( Pixels[][] maximums, int width, int height, double percent, int k ) throws NoSurfaceFoundException
- {
- int dimension = 0;
- // Setting and storage of the OS build in the X dimension according to the user thresholds settings.
- OSEStartingStatus startingStatus = new OSEStartingStatus( dimension );
- OSList[] osListsArrayX = new OSList[ height ];
- set( maximums, osListsArrayX, dimension, startingStatus );
-// displayOS(osListsArrayX);
- System.out.println( "OS.count = " + OSE.getCount() );
- /* Construction of the tempSurfaces*/
- ArrayList< Surface > surfaces =
- SurfacesReconstruction.buildSurfaces( 0, osListsArrayX, width, height, percent, k );
- if ( ! surfaces.isEmpty() )
- {
- mergeReferenceSurface( surfaces );
- }
- else
- {
- System.out.println( "No Surface Exception" );
- throw new FirstRoundConstructionException();
- }
- return surfaces;
- }
-
- /**
- * Rebuilds the double pixel array from the {@link SurfaceLine} array
- * of a {@link Surface} for a construction in the height dimension.
- *
- * @param surface - the {@link SurfaceLine} array of a {@link Surface}
- * @return a {@link Surface} specific double pixel array.
- */
- private static Pixels[][] rebuildPixelsArray( Surface surface, int width, int height )
- {
- Pixels[][] tempCoordinates = new Pixels[ width ][ height ]; // Transposed array
- for ( int i = 0; i <= height - 1; i++ )
- {
- for ( int j = 0; j <= width - 1; j++ )
- {
- if ( surface.get( i ) != null )
- {
- tempCoordinates[ j ][ i ] = surface.get( i ).get( j );
- }
- }
- }
- displayMaximums( tempCoordinates );
- return tempCoordinates;
- }
-
- /**
- * Converts and transposes the specified Surface object into the specified OSList array.
- *
- * @param surface - the Surface object to process
- * @param osListsArrayY -the output OSList array
- */
- private static void transposeSurfaceLines( Surface surface, OSList[] osListsArrayY, int width, int height )
- {
- int dimension = 1;
- Pixels[][] pixels = rebuildPixelsArray( surface, width, height );
- /* OS construction in dimension height.*/
- OSEStartingStatus startingStatus = new OSEStartingStatus( dimension );
- set( pixels, osListsArrayY, dimension, startingStatus );
- }
-
-
- /* ----- Other displaying methods -----*/
-
- /**
- * Reconstructs the TempSurface objects of the specified list in dimension width.
- *
- * @param surfaces - the list of TempSurface objects.
- * @return a list of reconstructed Tempsurface objects
- */
- private static ArrayList< Surface > secondRoundConstruction( ArrayList< Surface > surfaces, int width, int height, double percent, int k ) throws NoSurfaceFoundException
- {
- System.out.println( "========================================" );
- ArrayList< Surface > finalSurfaces = new ArrayList<>();
-
- for ( Surface surface : surfaces )
- {
- if ( surface.hasDuplicate() )// CoordinateList instead of Coordinate
- {
- OSList[] osListsArrayY = new OSList[ width ];
-
- transposeSurfaceLines( surface, osListsArrayY, width, height );
- OSE.setStartingStatus( 1 );
- System.out.println( "OS.count = " + OSE.getCount() );
-
-// displayOS( osListsArrayY );
- ArrayList< Surface > temps = SurfacesReconstruction.buildSurfaces( 1, osListsArrayY, width, height, percent, k );
- if ( temps.isEmpty() )
- {
- System.out.println( "small surface in second round" );
-// throw new SecondRoundConstructionException();
- }
- else
- {
- finalSurfaces.addAll( temps );
- }
- }
- else
- {
- finalSurfaces.add( surface.transpose() );
- }
- }
- mergeReferenceSurface( finalSurfaces );
- return finalSurfaces;
- }
- //TODO Handle the NOSurfaceFoundException dynamically : this particular surface has to be constructed with a
- // smaller StartingOSMinimumSize but not necessary the other ones.
- // May be add a static variable to store the maximum OS size per surfaces
- //
-
- /**
- * Merges the TempSurface objects of the specified list.
- *
- * @param surfaces - the list to merge
- */
- private static void mergeReferenceSurface( ArrayList< Surface > surfaces )
- {
- // Merging step.
- ArrayList< Surface > toRemoved = new ArrayList<>();
- for ( int i = surfaces.size() - 1; i > 0; i-- )
- {
- Surface one = surfaces.get( i );
- for ( int j = i - 1; j >= 0; j-- )
- {
- Surface two = surfaces.get( j );
- if ( one.sameSurface( two ) )
- {
- two.merge( one );
- toRemoved.add( one );
- }
- }
- }
- surfaces.removeAll( toRemoved );
- }
-
-
- private static < R extends RealType< R > & NativeType< R > > void projection(
- RandomAccessibleInterval< R > original, ImgFactory<R> factory, int delta, Img< UnsignedShortType > zMap,
- boolean zMapDisplay,
- boolean extractedStackDisplay,
- boolean heightMapDisplay,
- boolean projectionDisplay,
- String projectionType, int index )
- {
-
- // First step : fill in the holes. */
- Img< UnsignedShortType > interpolated = Interpolation.execute( zMap );
- Img< UnsignedShortType > smoothed = interpolated.copy();
- Utils.gaussConvolution( interpolated, smoothed, new double[]{ 1.0, 1.0 } );
-// Second step smoothed the elevation map
- if ( zMapDisplay )
- {
- ImageJFunctions.show( smoothed, "Elevation map" + "RS n°" + index );
- }
-
- Img< R > extractedStack = StackProjection.getExtractedStack( original, factory, smoothed, delta );
- if ( extractedStackDisplay )
- {
- ImageJFunctions.show( extractedStack,
- "Extracted stack (delta = " + delta + ")" + "RS n°" + index );
- }
- if ( projectionDisplay )
- {
- // A heightmap can be displayed
- if ( projectionType.equals( "MIP" ) ||
- projectionType.equals( "Minimum Intensity" ) )
- {
- Img< UnsignedShortType > heightMap = StackProjection.getHeightMap
- ( original, smoothed, projectionType, delta );
- if ( heightMapDisplay )
- {
- ImageJFunctions.show( heightMap, "Height Map with " +
- projectionType + " RS n°" + index );
- }
-
- Img< R > projection = StackProjection.projection1( original,factory, heightMap, projectionType );
- ImageJFunctions.show( projection, "Projection with " + projectionType + " RS n°" + index );
- }
- else
- {
-
- Img< R > projection = StackProjection.projection2( StackProjection.getHeightMapStack( original, factory,zMap, delta ),factory, projectionType );
- ImageJFunctions.show( projection, "Projection with " + projectionType + " RS n°" + index );
-
- }
-// ImageJFunctions.show(StackProjection.getHeightMapStack(original, zMap, delta), "HMS");
- }
-
- }
-
- /**
- * Displays the local maximums found using jzy3D package.
- */
- public static void displayMaximums( Pixels[][] maximums )
- {
- try
- {
- LocalMaximumsDisplay localMaximumsDisplay = new LocalMaximumsDisplay( maximums );
- AnalysisLauncher.open( localMaximumsDisplay );
- }
- catch ( Exception e )
- {
- e.printStackTrace();
- }
- }
-
- /**
- * Displays the local maximums found using jzy3D package.
- */
- public static void displayOS( OSList[] osLists )
- {
- try
- {
- OSDisplay display = new OSDisplay( osLists );
- AnalysisLauncher.open( display );
- }
- catch ( Exception e )
- {
- e.printStackTrace();
- }
- }
-
-
- public static void displaySurface( Surface surface )
- {
- try
- {
- SurfaceDisplay s = new SurfaceDisplay( surface );
- AnalysisLauncher.open( s );
- }
- catch ( Exception e )
- {
- e.printStackTrace();
- }
-
- }
-
-}
-
-
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacesReconstruction.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacesReconstruction.java
index 020be56967116bac4b3d82ce47198b5f2aa36b5d..35b57ad6fbf2238ebbd6f80d07cfad71f7474cbd 100644
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacesReconstruction.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/construction/SurfacesReconstruction.java
@@ -1,8 +1,8 @@
package fr.pasteur.ida.zellige.surfaceConstruction.construction;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSE;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSList;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ose.OSE;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ose.OSEList;
import fr.pasteur.ida.zellige.surfaceConstruction.element.Surface;
import fr.pasteur.ida.zellige.surfaceConstruction.element.surfaceLine.SurfaceLine;
import fr.pasteur.ida.zellige.surfaceConstruction.element.surfaceLine.SurfaceLineX;
@@ -17,33 +17,46 @@ import java.util.ArrayList;
public class SurfacesReconstruction
{
- private static int smallSurfaceCount;
+ private final ArrayList< Surface > surfaces = new ArrayList<>();
+ private final int dimension;
+ private final OSEList[] oseLists;
+ private final int surfaceLineLength;
+ private final double percent;
+ private final int k;
+
+ private int smallSurfaceCount;
+
+ public SurfacesReconstruction( int dimension, OSEList[] oseLists, int surfaceLineLength, double percent, int k )
+ {
+ this.dimension = dimension;
+ this.oseLists = oseLists;
+ this.surfaceLineLength = surfaceLineLength;
+ this.percent = percent;
+ this.k = k;
+ }
+
/**
* Returns a list of TempSurface constructed from the specified OSList array.
*
- * @param dimension - the dimension in which the construction have to be made.
- * @param osLists - the array of OSList
- * @return a list of TempSurface
*/
- public static ArrayList< Surface > buildSurfaces( int dimension, OSList[] osLists, int width, int height , double percent, int k)
+ public void buildSurfaces()
{
// Construction of the list of output TempSurface.
- ArrayList< Surface > surfaces = new ArrayList<>();
smallSurfaceCount = 0;
- int finalIndex = findIndexValue( osLists, 0, dimension, width, height );
+ int finalIndex = findIndexValue( 0 );
do
{
// All the OSLists are set to "not visited".
- reset( osLists );
+ reset();
int startingIndex = finalIndex;
- OSE firstOSE = getFirstOs( osLists, finalIndex );
+ OSE firstOSE = getFirstOs( finalIndex );
// osLists[finalIndex].remove( firstOS );//TODO remove or not
if ( firstOSE != null )
{
- Surface surface = createSurface( firstOSE, dimension, width, height);
- buildSurface( osLists, surface, finalIndex, width, height , percent, k);
+ Surface surface = createSurface( firstOSE, surfaceLineLength );
+ buildSurface( surface, finalIndex );
//it is really a reference surface ?
- if ( surface.getSize() >= width * height * 0.01 )
+ if ( surface.getSize() >= surfaceLineLength * oseLists.length * 0.01 )
{
surfaces.add( surface );
}
@@ -52,33 +65,30 @@ public class SurfacesReconstruction
smallSurfaceCount++;
System.out.println( "searching.....from " );
}
- finalIndex = findIndexValue( osLists, startingIndex, dimension, width, height );
+ finalIndex = findIndexValue( startingIndex );
}
}
- while ( finalIndex <= osLists.length - 2
- && ( osLists[ finalIndex ] != null
- && ! osLists[ finalIndex ].isEmpty()
- && osLists[ finalIndex ].containsAStart() ) );
- System.out.println( "Starting size = " + OSE.getStartingSize());
+ while ( finalIndex <= oseLists.length - 2
+ && ( oseLists[ finalIndex ] != null
+ && ! oseLists[ finalIndex ].isEmpty()
+ && oseLists[ finalIndex ].containsAStart() ) );
System.out.println( "smallSurfaceCount = " + smallSurfaceCount );
- return surfaces;
}
/**
* Adds new SurfaceLine to a specified TempSurface.
*
- * @param osLists - the OSList array in which to search
- * @param surface - the TempSurface to construct
- * @param index - the position in the TempSurface
+ * @param surface - the TempSurface to construct
+ * @param index - the position in the TempSurface
*/
- private static void buildSurface( OSList[] osLists, Surface surface, int index, int width, int height, double percent, int k )
+ private void buildSurface( Surface surface, int index )
{
/* First round of the construction -> top to bottom in the dimension.*/
SurfaceLine current = surface.get( index );
SurfaceLine next;
while ( current != null )
{
- next = searchForward( osLists, current, width, height , percent, k);
+ next = searchForward( current );
if ( next != null )
{
surface.set( next.getLine(), next );
@@ -91,11 +101,11 @@ public class SurfacesReconstruction
while ( size != surface.getSize() )
{
size = surface.getSize();
- for ( int i = surface.getLength() - 1; i > 0; i-- )
+ for ( int i = surface.getHeight() - 1; i > 0; i-- )
{
if ( surface.get( i ) != null )
{
- SurfaceLine previous = searchBackward( osLists, surface.get( i ), percent, k );
+ SurfaceLine previous = searchBackward( surface.get( i ) );
if ( previous != null )
{
if ( surface.get( i - 1 ) != null )
@@ -109,11 +119,11 @@ public class SurfacesReconstruction
}
}
}
- for ( int i = 0; i <= surface.getLength() - 2; i++ )
+ for ( int i = 0; i <= surface.getHeight() - 2; i++ )
{
if ( surface.get( i ) != null )
{
- next = searchForward( osLists, surface.get( i ), width, height , percent, k);
+ next = searchForward( surface.get( i ) );
if ( next != null )
{
if ( surface.get( i + 1 ) != null )
@@ -132,24 +142,23 @@ public class SurfacesReconstruction
/**
- * @param firstOSE - the first surface element.
- * @param dimension - the construction dimension
+ * @param firstOSE - the first surface element.
* @return a surface as a {@link Surface}
*/
- private static Surface createSurface( OSE firstOSE, int dimension, int width, int height)
+ private Surface createSurface( OSE firstOSE, int surfaceLineLength )
{
- Surface surface = new Surface( dimension, width, height );
+ Surface surface = new Surface( dimension, oseLists.length );
int i;
if ( dimension == 0 )
{
i = firstOSE.get( 0 ).getY();
- surface.set( i, new SurfaceLineX( width, firstOSE ) );
+ surface.set( i, new SurfaceLineX( surfaceLineLength, firstOSE ) );
}
else
{
i = firstOSE.get( 0 ).getX();
- surface.set( i, new SurfaceLineY(height, firstOSE ) );
+ surface.set( i, new SurfaceLineY( surfaceLineLength, firstOSE ) );
}
return surface;
}
@@ -157,28 +166,19 @@ public class SurfacesReconstruction
/**
* Returns the index value of the first OSList containing a starting OS.
*
- * @param osLists - the OSList array in which to search
- * @param index - the previous index value
- * @param dimension - the dimension in which the construction has to occur
+ * @param index - the previous index value
* @return the value of the first OSList containing a starting OS
*/
- private static int findIndexValue( OSList[] osLists, int index, int dimension, int width, int height )
+ private int findIndexValue( int index )
{
int i = index;
int limitValue;
- if ( dimension == 0 )
- {
- limitValue = height - 1;
- }
- else
- {
- limitValue = width - 1;
- }
+ limitValue = oseLists.length - 1;
while ( i <= limitValue - 2 )
{
- if ( osLists[ i ] != null
- && ! osLists[ i ].isEmpty()
- && osLists[ i ].containsAStart() )
+ if ( oseLists[ i ] != null
+ && ! oseLists[ i ].isEmpty()
+ && oseLists[ i ].containsAStart() )
{
return i;
}
@@ -191,13 +191,12 @@ public class SurfacesReconstruction
/**
* Returns the first OS with a start status in the OSList array.
*
- * @param osLists - the OSList array in which to search
- * @param index - the previous index value
+ * @param index the previous index value
* @return the first OS with a true Start status
*/
- private static OSE getFirstOs( OSList[] osLists, int index )
+ private OSE getFirstOs( int index )
{
- for ( OSE os : osLists[ index ] )
+ for ( OSE os : oseLists[ index ] )
{
if ( os.isAStart() )
{
@@ -216,20 +215,8 @@ public class SurfacesReconstruction
* @param j - the direction of the search (1 or -1)
* @return the OSList matching SurfaceLine
*/
- private static SurfaceLine search( OSList next, SurfaceLine currentLine, int j , double percent, int k)
- {// TODO USER PARAMETER
-// double percent;
-// int k;
-// if ( currentLine instanceof SurfaceLineX )
-// {
-// percent = 0.6;//TODO user parameter ?
-// k = 5;
-// }
-// else
-// {
-// percent = 0.7;
-// k = 2;
-// }
+ private SurfaceLine search( OSEList next, SurfaceLine currentLine, int j )
+ {
ArrayList< SurfaceLine > list = new ArrayList<>();
for ( OSE os : next )
{
@@ -257,25 +244,15 @@ public class SurfacesReconstruction
/**
* Returns the SurfaceLine generated from the specified OSList array matching the current SurfaceLine
*
- * @param osLists - the OSList array in which to search
- * @param current - the {@link SurfaceLine } to match
+ * @param current - the {@link SurfaceLine } to match
* @return the SurfaceLine generated from the specified OSList array matching the current SurfaceLine
*/
- private static SurfaceLine searchForward( OSList[] osLists, SurfaceLine current , int width, int height, double percent, int k)
+ private SurfaceLine searchForward( SurfaceLine current )
{
- int length;
- if ( current instanceof SurfaceLineX )
- {
- length = height;
- }
- else
- {
- length = width;
- }
- if ( current.getLine() + 1 <= length - 1 )
+ if ( current.getLine() + 1 <= oseLists.length - 1 )
{
- return search( osLists[ current.getLine() + 1 ], current, 1 , percent, k);
+ return search( oseLists[ current.getLine() + 1 ], current, 1 );
}
else
{
@@ -284,15 +261,14 @@ public class SurfacesReconstruction
}
/**
- * @param osLists - the {@link OSList} to search in.
- * @param current - the current SurfaceLine to match with.
+ * @param current - the current SurfaceLine to match with.
* @return - the matching SurfaceLine.
*/
- private static SurfaceLine searchBackward( OSList[] osLists, SurfaceLine current, double percent, int k)
+ private SurfaceLine searchBackward( SurfaceLine current )
{
if ( current.getCoordinatesNumber() != 0 && current.getLine() > 0 )
{
- return search( osLists[ current.getLine() - 1 ], current, - 1, percent, k );
+ return search( oseLists[ current.getLine() - 1 ], current, - 1 );
}
else
{
@@ -305,7 +281,7 @@ public class SurfacesReconstruction
*
* @param list - the list to merge.
*/
- private static void merge( ArrayList< SurfaceLine > list )
+ private void merge( ArrayList< SurfaceLine > list )
{
if ( list.size() >= 2 ) //more than one SurfaceLine
{
@@ -322,16 +298,25 @@ public class SurfacesReconstruction
/**
* Resets the "visited" value of each OS of each OSList to FALSE.
*
- * @param osLists - an array of {@link OSList} to reset.
*/
- private static void reset( OSList[] osLists )
+ private void reset()
{
- for ( OSList osList : osLists )
+ for ( OSEList oseList : oseLists )
{
- if ( osList != null )
+ if ( oseList != null )
{
- osList.reset();
+ oseList.reset();
}
}
}
+
+ public int getSmallSurfaceCount()
+ {
+ return smallSurfaceCount;
+ }
+
+ public ArrayList< Surface > getSurfaces()
+ {
+ return surfaces;
+ }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ReferenceSurface.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ReferenceSurface.java
new file mode 100644
index 0000000000000000000000000000000000000000..0ab013ec3ae2e4f4b2526dd83bdb68afc13c165c
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ReferenceSurface.java
@@ -0,0 +1,88 @@
+package fr.pasteur.ida.zellige.surfaceConstruction.element;
+
+import fr.pasteur.ida.zellige.surfaceConstruction.parameters.DisplayParameter;
+import fr.pasteur.ida.zellige.utils.StackProjection;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.img.Img;
+import net.imglib2.img.ImgFactory;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
+
+public class ReferenceSurface< T extends RealType< T > & NativeType< T > >
+{
+ private final RandomAccessibleInterval<T> input;
+ private final ImgFactory<T> factory;
+ private final Img< UnsignedShortType > zMap;
+ private Img<T> extractedStack;
+ private Img< UnsignedShortType > elevationMap;
+ private Img< T > projection;
+ private Img< T > heightMapStack;
+ private int index;
+ private int delta;
+ private String projectionType;
+
+
+ public ReferenceSurface( RandomAccessibleInterval<T> input,
+ ImgFactory<T> factory, Img< UnsignedShortType > zMap, int index)
+ {
+ this.input = input;
+ this.factory = factory;
+ this.zMap = zMap;
+ this.index = index;
+ }
+
+ public void setProjection( String projectionType, int delta)
+ {
+ this.delta = delta;
+ this.projectionType = projectionType;
+ ImageJFunctions.show( zMap, "input zMap" );
+ extractedStack = StackProjection.getExtractedStack( input, factory, zMap, delta );
+
+ if ( projectionType.equals( "MIP" ) ||
+ projectionType.equals( "Minimum Intensity" ) )
+ {
+ elevationMap = StackProjection.getElevationMap ( input, zMap, projectionType, delta );
+ projection = StackProjection.projection1( input,factory, elevationMap, projectionType );
+ }
+ else
+ {
+ heightMapStack = StackProjection.getHeightMapStack( input, factory,zMap, delta );
+ projection = StackProjection.projection2( heightMapStack,factory, projectionType );
+ }
+
+ }
+
+ public void display( DisplayParameter displayParameter )
+ {
+ if ( projection != null )
+ {
+ if ( displayParameter.iszMapDisplay() )
+ {
+ ImageJFunctions.show( zMap, "Elevation map" + "RS n°" + index );
+ }
+
+
+ if ( displayParameter.isExtractedStackDisplay() )
+
+ {
+ ImageJFunctions.show( extractedStack,
+ "Extracted stack (delta = " + delta + ")" + "RS n°" + index );
+ }
+ if ( displayParameter.isProjectionDisplay() )
+ {
+ ImageJFunctions.show( projection, "Projection with " + projectionType + " RS n°" + index );
+ // A heightmap can be displayed
+ }
+ if ( displayParameter.isElevationMapDisplay() )
+ {
+ ImageJFunctions.show( elevationMap, "Height Map with " +
+ projectionType + " RS n°" + index );
+ }
+ }
+ }
+
+}
+
+
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/Surface.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/Surface.java
index ec5214dcde63236e53432f61ec078858fc8e3f5f..9d460f5c639350e4d0552a7f9487f018e553c614 100644
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/Surface.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/Surface.java
@@ -1,6 +1,6 @@
package fr.pasteur.ida.zellige.surfaceConstruction.element;
-import fr.pasteur.ida.zellige.surfaceConstruction.construction.SurfacesExtraction;
+import fr.pasteur.ida.zellige.surfaceConstruction.construction.ReferenceSurfaceExtraction;
import fr.pasteur.ida.zellige.surfaceConstruction.element.surfaceLine.SurfaceLine;
import fr.pasteur.ida.zellige.surfaceConstruction.element.surfaceLine.SurfaceLineX;
import fr.pasteur.ida.zellige.surfaceConstruction.element.surfaceLine.SurfaceLineY;
@@ -9,6 +9,7 @@ import net.imglib2.FinalDimensions;
import net.imglib2.RandomAccess;
import net.imglib2.img.Img;
import net.imglib2.img.ImgFactory;
+import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.util.Util;
@@ -19,23 +20,10 @@ public class Surface
private final SurfaceLine[] surfaceLines;
private final int dimension;
- private final int width;
- private final int height;
- public Surface( int dimension, int width, int height )
+ public Surface( int dimension, int length )
{
- this.width = width;
- this.height = height;
- int length;
- if ( dimension == 0 )
- {
- length = height;
- }
- else
- {
- length = width;
- }
this.dimension = dimension;
this.surfaceLines = new SurfaceLine[ length ];
}
@@ -48,7 +36,7 @@ public class Surface
*/
public boolean hasDuplicate()
{
- for ( int i = 0; i <= this.getLength() - 1; i++ )
+ for ( int i = 0; i <= this.getHeight() - 1; i++ )
{
SurfaceLine s = this.get( i );
if ( s != null && s.hasDuplicate() )
@@ -122,7 +110,7 @@ public class Surface
{
int count = 0;
int common = 0;
- for ( int i = 0; i <= this.getLength() - 1; i++ )
+ for ( int i = 0; i <= this.getHeight() - 1; i++ )
{
if ( this.get( i ) != null && other.get( i ) != null )// There is a SurfaceLine at index i in both TempSurface
{
@@ -143,7 +131,7 @@ public class Surface
*/
public void merge( Surface otherSurface )
{
- for ( int i = 0; i <= this.getLength() - 1; i++ )
+ for ( int i = 0; i <= this.getHeight() - 1; i++ )
{
if ( this.get( i ) != null &&
otherSurface.get( i ) != null &&
@@ -159,23 +147,21 @@ public class Surface
*
* @return the identical transposed {@link Surface}
*/
- public Surface transpose()
+ public Surface transpose(int length)
{
- Surface surface = new Surface( Math.abs( this.dimension - 1 ), width, height );
+ Surface surface = new Surface( Math.abs( this.dimension - 1 ), length );
Class< ? > theClass;
- int length;
+
if ( this.dimension == 0 )
{
theClass = SurfaceLineY.class;
- length = height;
}
else
{
theClass = SurfaceLineX.class;
- length = width;
}
- for ( int i = 0; i <= this.getLength() - 1; i++ )
+ for ( int i = 0; i <= this.getHeight() - 1; i++ )
{
SurfaceLine surfaceLine = this.get( i );
if ( surfaceLine != null )
@@ -243,8 +229,9 @@ public class Surface
public Img< UnsignedShortType > getZMap()
{
+ ReferenceSurfaceExtraction.displaySurface( this );
int count = 0;
- Dimensions dim = FinalDimensions.wrap( new long[]{width,height });
+ Dimensions dim = FinalDimensions.wrap( new long[]{surfaceLines.length,surfaceLines[0].getLength() });
ImgFactory< UnsignedShortType > factory = Util.getArrayOrCellImgFactory(dim, new UnsignedShortType());
Img< UnsignedShortType > zMap = factory.create(dim);
RandomAccess< UnsignedShortType > randomAccess = zMap.randomAccess();
@@ -278,6 +265,7 @@ public class Surface
}
}
}
+ ImageJFunctions.show( zMap, "after getzmap" );
System.out.println(" Thre count = " + count);
return zMap;
}
@@ -319,7 +307,7 @@ public class Surface
- public int getLength()
+ public int getHeight()
{
return this.surfaceLines.length;
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/os/OSE.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ose/OSE.java
similarity index 67%
rename from src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/os/OSE.java
rename to src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ose/OSE.java
index db4332f6ed6612c9fbe91d4b5c26185449fe66b8..eeddbe41f8c6d65723c4691953535537e58d2670 100644
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/os/OSE.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ose/OSE.java
@@ -1,4 +1,4 @@
-package fr.pasteur.ida.zellige.surfaceConstruction.element.os;
+package fr.pasteur.ida.zellige.surfaceConstruction.element.ose;
import fr.pasteur.ida.zellige.surfaceConstruction.element.Coordinate;
@@ -10,14 +10,10 @@ import java.util.*;
*/
public class OSE extends ArrayList< Coordinate >
{
- private static TreeSet <Integer> list = new TreeSet<>();
- private static TreeMap<Integer, Integer> occ = new TreeMap<>();
- private static int startingSize;
- private OSEStartingStatus startingStatus;
-
+ public static int sizeSum = 0;
/* Not necessary for the program.*/
private static int count = 0;
- public static int sizeSum = 0;
+ private final OSEStartingStatus startingStatus;
private int name;
/*-------------*/
@@ -30,47 +26,32 @@ public class OSE extends ArrayList< Coordinate >
*/
private boolean start = true;
- public OSE(OSEStartingStatus startingStatus )
+ public OSE( OSEStartingStatus startingStatus )
{
this.startingStatus = startingStatus;
}
+ public static int getCount()
+ {
+ return count;
+ }
+
/**
* Sets the start status to false if the size is inferior to the OS start minimum size.
* Default value = 70 Pixels.
* {@link Coordinate} of the OS
*/
- public void set( )
+ public void set()
{
- list.add( this.size() );
-
-
- /* Not necessary for the program.*/
- this.name = count;
- /*----------------*/
- sizeSum = sizeSum + this.size();
- count++;
- }
-
- public void set( int dimension )
- {
- list.add( this.size() );
- Integer j = startingStatus.get(this.size() );
-
+ Integer j = startingStatus.get( this.size() );
+ startingStatus.put( this.size(), ( j == null ) ? 1 : j + 1 );
/* Not necessary for the program.*/
this.name = count;
/*----------------*/
sizeSum = sizeSum + this.size();
count++;
-
-// if(dimension == 0)
- startingStatus.put( this.size(), ( j == null ) ? 1 : j + 1 );
-
-
-
}
-
/**
* Test if the current instance is adjacent to the next OS instance.
*
@@ -96,7 +77,6 @@ public class OSE extends ArrayList< Coordinate >
}
}
-
/**
* Returns true if the OS has been visited.
*
@@ -107,16 +87,6 @@ public class OSE extends ArrayList< Coordinate >
return visited;
}
- /**
- * Sets the visited status to true (the instance belongs to a ReferenceSurface)
- * and therefore sets the start status to false.
- */
- public void setVisited()
- {
- this.visited = true;
- this.start = false;
- }
-
/**
* Sets the visited parameter to the specified value.
*
@@ -127,6 +97,15 @@ public class OSE extends ArrayList< Coordinate >
this.visited = visited;
}
+ /**
+ * Sets the visited status to true (the instance belongs to a ReferenceSurface)
+ * and therefore sets the start status to false.
+ */
+ public void setVisited()
+ {
+ this.visited = true;
+ this.start = false;
+ }
/**
* Indicates whether some other object is "equal to" this one
@@ -153,12 +132,7 @@ public class OSE extends ArrayList< Coordinate >
*/
public boolean isAStart()
{
- return (this.size() >= this.startingStatus.getMinimumSize() && start);
- }
-
- public boolean isAStart(int minimumSize)
- {
- return (this.size() >= this.startingStatus.getMinimumSize() && start);
+ return ( this.size() >= this.startingStatus.getMinimumSize() && start );
}
/* Not necessary for the program.*/
@@ -167,54 +141,4 @@ public class OSE extends ArrayList< Coordinate >
return ( " " + name );
}
-public static void setStartingStatus(int dimension)
-{
- //TODO user parameter ?
- if (list.size() != 0)
- {
- startingSize = 0;
- if ( dimension == 0 )
- {
- for ( int i = 0; list.size() > 20 && i <= list.size()* 0.75 ;i++ )
- {
- list.remove( list.last() );
- }
- }
- else
- {
- for ( int i = 0; list.size() > 2 && i <= list.size() / 10; i++ )
- {
- list.remove( list.last() );
- }
- }
- startingSize = list.last();
- list = new TreeSet<>();
- }}
-
-
- public static void setStartingStatusStats(int dimension)
- {
- startingSize = list.last();
-}
-
-
- public static int getCount()
- {
- return count;
- }
-
- public static void setCount( int count )
- {
- OSE.count = count;
- }
-
- public TreeMap< Integer, Integer > getOcc()
- {
- return startingStatus;
- }
-
- public static int getStartingSize()
- {
- return startingSize;
- }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/os/OSList.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ose/OSEList.java
similarity index 91%
rename from src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/os/OSList.java
rename to src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ose/OSEList.java
index 1bfe8bc40680120bf0ca0ecf84f478cf503d16f2..c1c69856fc4ffbaff319ea3cb47e10b3cf8edf3f 100644
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/os/OSList.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ose/OSEList.java
@@ -1,4 +1,4 @@
-package fr.pasteur.ida.zellige.surfaceConstruction.element.os;
+package fr.pasteur.ida.zellige.surfaceConstruction.element.ose;
import java.util.ArrayList;
import java.util.Collection;
@@ -6,11 +6,11 @@ import java.util.Collection;
/**
* An OSList object is simply an ArrayList of {@link OSE}
*/
-public class OSList extends ArrayList < OSE >
+public class OSEList extends ArrayList < OSE >
{
- public OSList( )
+ public OSEList( )
{
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/os/OSEStartingStatus.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ose/OSEStartingStatus.java
similarity index 93%
rename from src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/os/OSEStartingStatus.java
rename to src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ose/OSEStartingStatus.java
index 05c93286a6ce162b9aab7544dbcb3a3368536304..be3f4c2906574bb0fac1b2df050b34369c97338a 100644
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/os/OSEStartingStatus.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/ose/OSEStartingStatus.java
@@ -1,4 +1,4 @@
-package fr.pasteur.ida.zellige.surfaceConstruction.element.os;
+package fr.pasteur.ida.zellige.surfaceConstruction.element.ose;
import java.util.TreeMap;
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/surfaceLine/SurfaceLine.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/surfaceLine/SurfaceLine.java
index c6f098045f624414a96eefdef2f22cb0a8de77ba..54321fb750330488b0fa68f5a2f988cd11a30b23 100644
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/surfaceLine/SurfaceLine.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/surfaceLine/SurfaceLine.java
@@ -2,8 +2,7 @@ package fr.pasteur.ida.zellige.surfaceConstruction.element.surfaceLine;
import fr.pasteur.ida.zellige.surfaceConstruction.element.Coordinate;
import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSE;
-import fr.pasteur.ida.zellige.surfaceConstruction.construction.SurfacesExtraction;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ose.OSE;
public abstract class SurfaceLine
{
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/surfaceLine/SurfaceLineX.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/surfaceLine/SurfaceLineX.java
index 1fa11ca2cefd0c6d4625e836d85344c35649e4c1..9fe02a4d25843339ccdf4aaa82439701bdfaed4d 100644
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/surfaceLine/SurfaceLineX.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/surfaceLine/SurfaceLineX.java
@@ -1,7 +1,7 @@
package fr.pasteur.ida.zellige.surfaceConstruction.element.surfaceLine;
import fr.pasteur.ida.zellige.surfaceConstruction.element.Coordinate;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSE;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ose.OSE;
public class SurfaceLineX extends SurfaceLine
{
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/surfaceLine/SurfaceLineY.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/surfaceLine/SurfaceLineY.java
index be9f4b50d684fc29ee8a30924c669ce597b5d4c1..9204b511cf3cdbfd54b4bc70a0eeda5065000278 100644
--- a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/surfaceLine/SurfaceLineY.java
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/element/surfaceLine/SurfaceLineY.java
@@ -1,7 +1,7 @@
package fr.pasteur.ida.zellige.surfaceConstruction.element.surfaceLine;
import fr.pasteur.ida.zellige.surfaceConstruction.element.Coordinate;
-import fr.pasteur.ida.zellige.surfaceConstruction.element.os.OSE;
+import fr.pasteur.ida.zellige.surfaceConstruction.element.ose.OSE;
public class SurfaceLineY extends SurfaceLine
{
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/parameters/AdvancedUserParameters.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/parameters/AdvancedUserParameters.java
new file mode 100644
index 0000000000000000000000000000000000000000..1f91632024362c725cdfba3dca8391f57afff9c2
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/parameters/AdvancedUserParameters.java
@@ -0,0 +1,57 @@
+package fr.pasteur.ida.zellige.surfaceConstruction.parameters;
+
+public class AdvancedUserParameters
+{
+ private int k1;
+ private double percent1;
+ private int k2;
+ private double percent2;
+
+ public AdvancedUserParameters( int k1, double percent1, int k2, double percent2 )
+ {
+ this.k1 = k1;
+ this.percent1 = percent1;
+ this.k2 = k2;
+ this.percent2 = percent2;
+ }
+
+ public int getK1()
+ {
+ return k1;
+ }
+
+ public void setK1( int k1 )
+ {
+ this.k1 = k1;
+ }
+
+ public double getPercent1()
+ {
+ return percent1;
+ }
+
+ public void setPercent1( double percent1 )
+ {
+ this.percent1 = percent1;
+ }
+
+ public int getK2()
+ {
+ return k2;
+ }
+
+ public void setK2( int k2 )
+ {
+ this.k2 = k2;
+ }
+
+ public double getPercent2()
+ {
+ return percent2;
+ }
+
+ public void setPercent2( double percent2 )
+ {
+ this.percent2 = percent2;
+ }
+}
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/parameters/DisplayParameter.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/parameters/DisplayParameter.java
new file mode 100644
index 0000000000000000000000000000000000000000..5b0ad5983b06cc04ccc55cfc7424160a777cc3d3
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/parameters/DisplayParameter.java
@@ -0,0 +1,40 @@
+package fr.pasteur.ida.zellige.surfaceConstruction.parameters;
+
+public class DisplayParameter
+{
+
+ private final boolean zMapDisplay;
+ private final boolean extractedStackDisplay;
+ private final boolean elevationMapDisplay;
+ private final boolean projectionDisplay;
+ private final int delta;
+
+ public DisplayParameter(int delta, boolean zMapDisplay, boolean extractedStackDisplay, boolean elevationMapDisplay, boolean projectionDisplay )
+ {
+ this.delta = delta;
+ this.zMapDisplay = zMapDisplay;
+ this.extractedStackDisplay = extractedStackDisplay;
+ this.elevationMapDisplay = elevationMapDisplay;
+ this.projectionDisplay = projectionDisplay;
+ }
+
+ public boolean iszMapDisplay()
+ {
+ return zMapDisplay;
+ }
+
+ public boolean isExtractedStackDisplay()
+ {
+ return extractedStackDisplay;
+ }
+
+ public boolean isElevationMapDisplay()
+ {
+ return elevationMapDisplay;
+ }
+
+ public boolean isProjectionDisplay()
+ {
+ return projectionDisplay;
+ }
+}
diff --git a/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/parameters/UserParameters.java b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/parameters/UserParameters.java
new file mode 100644
index 0000000000000000000000000000000000000000..f9a48c64817e1cb8a31776a14076d8f5596d1cfc
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/surfaceConstruction/parameters/UserParameters.java
@@ -0,0 +1,72 @@
+package fr.pasteur.ida.zellige.surfaceConstruction.parameters;
+
+public class UserParameters
+{
+
+ private double amplitude;
+ private double threshold;
+ private int sigmas;
+ private int delta;
+ private String projectionType;
+
+
+ public UserParameters( double amplitude, double threshold, int sigmas, int delta , String projectionType)
+ {
+ this.amplitude = amplitude;
+ this.threshold = threshold;
+ this.sigmas = sigmas;
+ this.delta = delta;
+ this.projectionType = projectionType;
+
+ }
+
+ public double getAmplitude()
+ {
+ return amplitude;
+ }
+
+ public void setAmplitude( double amplitude )
+ {
+ this.amplitude = amplitude;
+ }
+
+ public double getThreshold()
+ {
+ return threshold;
+ }
+
+ public void setThreshold( double threshold )
+ {
+ this.threshold = threshold;
+ }
+
+ public int getSigmas()
+ {
+ return sigmas;
+ }
+
+ public void setSigmas( int sigmas )
+ {
+ this.sigmas = sigmas;
+ }
+
+ public int getDelta()
+ {
+ return delta;
+ }
+
+ public void setDelta( int delta )
+ {
+ this.delta = delta;
+ }
+
+ public String getProjectionType()
+ {
+ return projectionType;
+ }
+
+ public void setProjectionType( String projectionType )
+ {
+ this.projectionType = projectionType;
+ }
+}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/BasePixFilter.java b/src/main/java/fr/pasteur/ida/zellige/utils/BasePixFilter.java
deleted file mode 100644
index 872a4e4e0ef35dbbd10fe64ef9f7cd357ca358db..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/utils/BasePixFilter.java
+++ /dev/null
@@ -1,126 +0,0 @@
-package fr.pasteur.ida.zellige.utils;
-
-
-import net.imglib2.Cursor;
-import net.imglib2.IterableInterval;
-import net.imglib2.RandomAccess;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.algorithm.neighborhood.CenteredRectangleShape;
-import net.imglib2.algorithm.neighborhood.Neighborhood;
-import net.imglib2.algorithm.neighborhood.RectangleShape;
-import net.imglib2.algorithm.neighborhood.RectangleShape.NeighborhoodsAccessible;
-import net.imglib2.img.Img;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.view.IntervalView;
-import net.imglib2.view.Views;
-
-import static net.imglib2.util.ImgUtil.copy;
-
-
-//TODO Javadoc
-
-/**
- * @param <T> the type of the source image.
- * @author Céline Trébeau - 2020
- */
-public class BasePixFilter<T extends RealType<T> & NativeType<T>> {
-
-
- public static <T extends RealType<T> & NativeType<T>> Img<T> run(Img<T> source) {
- BasePixOperator<T> basePixOperator = new BasePixOperator<>( source);
- basePixOperator.process();
- return basePixOperator.getResult();
- }
-
-
- private static class BasePixOperator<T extends RealType<T> & NativeType<T>> {
- private final Img<T> source;
-
- private final Img<T> output;
-
-
-
-
- /**
- * Instantiate a new median filter that will operate on the specified
- * source.
- *
- * @param source the source to operate on.
- */
- public BasePixOperator(final Img<T> source) {
- this.source = source;
- this.output = source.factory().create(source);
- copy(source, output);
- }
-
- // public void process() {
-//
-// Img<T> temp = source.factory().create(source);//TODO may be 2 different neighbour number to reduce the iteration
-// copy(source,temp);
-//
-// for(int i = 0 ; i <= iter - 1; i ++)
-// {
-// process(temp, output, n);
-// temp = output.copy();
-//// ImageJFunctions.show( output, "iteration "+ i );
-// }
-// }
- public void process() {
- for (int z = 0; z < source.dimension(2); z++) {//TODO why use long ?
- final IntervalView<T> slice = Views.hyperSlice(source, 2, z);
- final IntervalView<T> outputSlice = Views.hyperSlice(output, 2, z);
- processSlice(slice, outputSlice);
-
- }
-// System.out.println("-------------------------" );
- }
-
-
- private void processSlice(final RandomAccessibleInterval<T> in, final IterableInterval<T> out) {
- final Cursor<T> cursor = out.cursor();
- final CenteredRectangleShape shape = new CenteredRectangleShape(new int[]{1, 2}, false);
- final CenteredRectangleShape shape2 = new CenteredRectangleShape(new int[]{2, 1}, false);
- final NeighborhoodsAccessible<T> accessible = shape.neighborhoodsRandomAccessible(Views.extendZero(in));
- final NeighborhoodsAccessible<T> accessible2 = shape.neighborhoodsRandomAccessible(Views.extendZero(in));
- final RandomAccess<Neighborhood<T>> nra1 = accessible.randomAccess(in);
- final RandomAccess<Neighborhood<T>> nra2 = accessible.randomAccess(in);
- int count = 0;
-
-// final int size = (int) nra.get().size();
- // Fill buffer with median values.
- while (cursor.hasNext()) {
- int values = 0;
- int values2 = 0;
- cursor.fwd();
- if (cursor.get().getRealFloat() != 0) {
- nra1.setPosition(cursor);
- nra2.setPosition(cursor);
- for (final T pixel : nra1.get()) {
- if (pixel.getRealFloat() > 0) {
- values++;
- }
- }
- for (final T pixel : nra2.get()) {
- if (pixel.getRealFloat() > 0) {
- values2++;
- }
- }
-
- if (values < 6 && values2 <6) {
- cursor.get().setReal(0);
- count++;
- }
- }
-
- }
-// System.out.println(count + " pixels removed");
- }
-
-
- public Img<T> getResult() {
- return output;
- }
-
- }
-}
\ No newline at end of file
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/Filter2D.java b/src/main/java/fr/pasteur/ida/zellige/utils/Filter2D.java
deleted file mode 100644
index 0974e99fbca6d94d95edf84a0c8da4c640a12b01..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/utils/Filter2D.java
+++ /dev/null
@@ -1,182 +0,0 @@
-package fr.pasteur.ida.zellige.utils;
-
-import ij.IJ;
-import net.imglib2.Cursor;
-import net.imglib2.IterableInterval;
-import net.imglib2.RandomAccess;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.algorithm.neighborhood.Neighborhood;
-import net.imglib2.algorithm.neighborhood.RectangleShape;
-import net.imglib2.img.Img;
-import net.imglib2.img.display.imagej.ImageJFunctions;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.view.IntervalView;
-import net.imglib2.view.Views;
-
-import java.util.Arrays;
-
-public class Filter2D<T extends RealType<T> & NativeType<T>> {
-
-
- public static <T extends RealType<T> & NativeType<T>> Img<T> median(final Img<T> source, final int radius) {
- Process<T> p = new Process<>(source, radius, "median");
- p.run();
- return p.output;
- }
-
- public static <T extends RealType<T> & NativeType<T>> Img<T> variance(final Img<T> source, final int radius) {
- Process<T> p = new Process<>(source, radius, "variance");
- p.run();
- return p.output;
- }
-
- public static <T extends RealType<T> & NativeType<T>> Img<T> SD(final Img<T> source, final int radius) {
- Process<T> p = new Process<>(source, radius, "sd");
- p.run();
- return p.output;
- }
-
- public static <T extends RealType<T> & NativeType<T>> Img<T> mean(final Img<T> source, final int radius) {
- Process<T> p = new Process<>(source, radius, "mean");
- p.run();
-
- return p.output;
- }
-
- public static class Process<T extends RealType<T> & NativeType<T>> {
- private final Img<T> source;
-
- private final Img<T> output;
-
- private final int radius;
- private final String method;
-
- public Process(Img<T> source, int radius, String method) {
- this.source = source;
- this.radius = radius;
- this.output = source.factory().create(source.dimension(0), source.dimension(1), source.dimension(2));
- this.method = method;
- }
-
- public void run() {
- final long nz = source.dimension(2);
- for (long z = 0; z < nz; z++) {
- final IntervalView<T> slice = Views.hyperSlice(source, 2, z);
- final IntervalView<T> outputSlice = Views.hyperSlice(output, 2, z);
- ProcessSlice<T> p = new ProcessSlice<>(slice, outputSlice, radius);
- p.run(method);
- }ImageJFunctions.show( output.copy(), method );
- }
-
- }
-
- public static class ProcessSlice<T extends RealType<T> & NativeType<T>> {
-
- final Cursor<T> cursor;
- final RandomAccess<Neighborhood<T>> nra;
-
- private ProcessSlice(final RandomAccessibleInterval<T> in, final IterableInterval<T> out, int radius) {
- cursor = out.cursor();
- final RectangleShape shape = new RectangleShape(radius, false);
- final RectangleShape.NeighborhoodsAccessible<T> accessible = shape.neighborhoodsRandomAccessible(Views.extendZero(in));
- nra = accessible.randomAccess(in);
-
-
- }
-
- private void run(String method) {
- final int size = (int) nra.get().size();
- final double[] values = new double[size];
- while (cursor.hasNext()) {
- cursor.fwd();
- nra.setPosition(cursor);
- double v = 0;
- if (method.endsWith("mean")) {
- v = computeMean(nra, values);
- } else if (method.equals("median")) {
- v = computeMedian(nra, values);
- } else if (method.equals("sd")) {
- v = computeSD(nra, values);
- } else if (method.equals("variance")) {
- v = computeVariance(nra, values);
- } else {
- IJ.log("This method doesn't exist, try something else");
- }
-
- cursor.get().setReal(v); /* Not variance but SD*/
- }
- }
- }
-
- public static <T extends RealType<T> & NativeType<T>> double
- computeMean(RandomAccess<Neighborhood<T>> nra, double[] values) {
- int index = 0;
- double sum = 0;
- for (final T pixel : nra.get()) {
- double value = pixel.getRealDouble();
- if(value != 0)
- {
- values[ index ] = value;
- sum = sum + value;
- index++;
- }
- }
- return sum / (index);
-
- }
-
- public static <T extends RealType<T> & NativeType<T>> double
- computeSD(RandomAccess<Neighborhood<T>> nra, double[] values) {
- int index = 0;
- double sum = 0;
- for (final T pixel : nra.get()) {
- double value = pixel.getRealDouble();
- values[index] = value;
- sum = sum + value;
- index++;
- }
- double mean = sum / (index);
- return Math.sqrt(computeVariance(values, mean));
- }
-
- public static <T extends RealType<T> & NativeType<T>> double
- computeMedian(RandomAccess<Neighborhood<T>> nra, double[] values) {
- int index = 0;
- double sum = 0;
- for (final T pixel : nra.get()) {
- double value = pixel.getRealDouble();
- values[index] = value;
- sum = sum + value;
- index++;
- }
- Arrays.sort(values, 0, index);
- return values[(index - 1) / 2];
- }
-
- public static <T extends RealType<T> & NativeType<T>> double
- computeVariance(RandomAccess<Neighborhood<T>> nra, double[] values) {
- int index = 0;
- double sum = 0;
- for (final T pixel : nra.get()) {
- double value = pixel.getRealDouble();
- values[index] = value;
- sum = sum + value;
- index++;
- }
- double mean = sum / (index);
- return computeVariance(values, mean);
- }
-
-
- public static double computeVariance(double[] values, double mean) {
- double variance = 0;
- for (int i = 0; i <= values.length - 1; i++) {
- double v = values[i] - mean;
- double vSquare = v * v;
- variance = variance + (vSquare);
- }
- return variance / values.length;
-
- }
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/Histogram2D.java b/src/main/java/fr/pasteur/ida/zellige/utils/Histogram2D.java
deleted file mode 100644
index b4410140173d9bebe7da7ce3fa8134f105f8932f..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/utils/Histogram2D.java
+++ /dev/null
@@ -1,81 +0,0 @@
-package fr.pasteur.ida.zellige.utils;
-
-import net.imglib2.Cursor;
-import net.imglib2.RandomAccess;
-import net.imglib2.img.Img;
-import net.imglib2.img.display.imagej.ImageJFunctions;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-
-public class Histogram2D < T extends RealType< T > & NativeType< T >>{
-
- Img<T> img1, img2;
- int [][] histogram;
-// int [] binNums;
- double [] min;
- double [] max;
-
-
- public Histogram2D(Img<T> img1, Img <T> img2, int bin1, int bin2, boolean zero, boolean zero2) {
- this.img1 = img1;
- this.img2 = img2;
- histogram = new int[bin2][bin1];
- double min1 = Threshold.findMin(this.img1, zero).getRealDouble();
- double min2 = Threshold.findMin(this.img2, zero2).getRealDouble() ;
- min = new double[]{min1, min2};
-
- double max1 = Threshold.findMax(this.img1).getRealDouble();
- double max2 = Threshold.findMax(this.img2).getRealDouble();
- max = new double[]{max1, max2};
- }
-
- public void process()
- {
- final Cursor <T> cursor1 = img1.localizingCursor();
- final Cursor <T> cursor2 = img2.cursor();
- double binWidth1 = (max[0] - min[0])/ histogram[0].length ;
- double binWidth2 = (max[1] - min[1])/ histogram.length ;
- while (cursor1.hasNext())
- {
- cursor1.fwd();
- cursor2.fwd();
-
- final double t1 = cursor1.get().getRealDouble();final double t2 = cursor2.get().getRealDouble();
- if (t1 != 0 && t2!= 0) {
-
- int index0 = (int) ((t1 - min[0]) / binWidth1);
- int index1 = (int) ((t2 - min[1]) / binWidth2);
- try {
- histogram[index1][index0]++;
- } catch (ArrayIndexOutOfBoundsException a) {
- if (index0 == histogram[0].length) {
- index0 = histogram[0].length - 1;
- }
- if (index1 == histogram.length) {
- index1 = histogram.length - 1;
- }
- histogram[index1][index0]++;
-
- }
- }
-
- }
- }
-
- public void display()
- {
- Img<T> hist = img1.factory().create(histogram[0].length, histogram.length);
- RandomAccess <T> randomAccess = hist.randomAccess();
- for(int i = 0; i <= histogram[0].length - 1; i++)
- {
- for (int j = 0; j <= histogram.length - 1; j++)
- {
- final T value = Utils.setPositionAndGet(randomAccess, i, j);
- if (histogram[j][i] != 0)
-// value.setReal(100);
- value.setReal(histogram[j][i]);
- }
- }
- ImageJFunctions.show(hist, "histogram");
- }
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/Interpolation.java b/src/main/java/fr/pasteur/ida/zellige/utils/Interpolation.java
index 034e03afb3d10854259420db77eb3317e1db4b77..76a1a0a6bcb10d75ee0f9d30a1abda5701cf368b 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/Interpolation.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/Interpolation.java
@@ -2,200 +2,226 @@ package fr.pasteur.ida.zellige.utils;
import net.imglib2.Cursor;
import net.imglib2.RandomAccess;
+import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
+import net.imglib2.img.ImgFactory;
+import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.numeric.integer.UnsignedShortType;
+import net.imglib2.util.ImgUtil;
/**
* @author ctrebeau
- * Methods to perform 2D linear interpolation on a 2D {@link Double } array.
+ * Methods to perform 2D linear interpolation on a 2D {@link Img<UnsignedShortType> }.
*/
public class Interpolation
{
- /**
- * Determines the slope of the linear equation y = ax + b given 2 points P1(x1, y1) and P2 (x2, y2).
- *
- * @param x1 - x coordinates for the first point.
- * @param x2 - x coordinates for the second point.
- * @param z1 - z coordinates for the first point.
- * @param z2 - z coordinates for the second point.
- * @return the slope of the linear equation y = ax + b.
- */
- private static double getA( int x1, int x2, double z1, double z2 )
+ public static Img<UnsignedShortType> run( RandomAccessibleInterval< UnsignedShortType > input )
{
- return ( z2 - z1 ) / ( double ) ( x2 - x1 );
+ InterpolationOperator operator = new InterpolationOperator( input );
+ ImageJFunctions.show( operator.getOutput() );
+ return operator.getOutput();
}
+ public static class InterpolationOperator
+ {
+ private final RandomAccessibleInterval< UnsignedShortType > input;
+ private Img < UnsignedShortType > output;
- /**
- * Determines the constant b of the linear equation y = ax + b given one point P1(x1, y1) and the slope a.
- *
- * @param a - the slope a of the linear equation y = ax + b.
- * @param x1 - x coordinates for the first point.
- * @param z1 - z coordinates for the first point.
- * @return the b constant of the linear equation y = ax + b.
- */
- private static double getB( double a, int x1, double z1 )
- {
- return z1 - ( a * x1 );
- }
+ public InterpolationOperator( RandomAccessibleInterval< UnsignedShortType > input )
+ {
+ this.input = input;
+ execute();
+ }
+ /**
+ * Returns an interpolated version of the specified image.
+ * The interpolation is the mean of the interpolated image in both dimensions dimension.
+ */
+ private void execute()
+ {
+ ImageJFunctions.show( input, "zMap" );
+ Img< UnsignedShortType > interpolated0 = execute( input, 0 );
+ ImageJFunctions.show( interpolated0, "interpolated 0" );
+ Img< UnsignedShortType > interpolated1 = execute( input, 1 );
+ ImageJFunctions.show( interpolated1, "interpolated 1" );
+ Cursor< UnsignedShortType > cursor0 = interpolated0.cursor();
+ Cursor< UnsignedShortType > cursor1 = interpolated1.cursor();
+
+ while ( cursor0.hasNext() )
+ {
+ cursor0.fwd();
+ cursor1.fwd();
+ int type0 = cursor0.get().getInteger();
+ int type1 = cursor1.get().getInteger();
+ if ( type0 != 0 )
+ {
+ if ( type1 != 0 )
+ {
+ cursor0.get().set( ( type0 + type1 ) / 2 );
+ }
+ }
+ else if ( type1 != 0 )
+ {
+ cursor0.get().set( cursor1.get() );
+ }
+ }
+ this.output = interpolated0;
+ }
- /**
- * Determines the unknown z coordinate of a point P given its x coordinate,
- * the slope and the constant of the linear equation y = ax + b.
- *
- * @param a - the slope a of the linear equation y = ax + b.
- * @param b - the b constant of the linear equation y = ax + b.
- * @param x - the x coordinate of a point with unknown z coordinate.
- * @return - the z coordinate corresponding to the x coordinate.
- */
- private static int executeInt( double a, double b, int x )
- {
- return ( int ) Math.round( a * x + b );
- }
+ /**
+ * Determines the slope of the linear equation y = ax + b given 2 points P1(x1, y1) and P2 (x2, y2).
+ *
+ * @param x1 - x coordinates for the first point.
+ * @param x2 - x coordinates for the second point.
+ * @param z1 - z coordinates for the first point.
+ * @param z2 - z coordinates for the second point.
+ * @return the slope of the linear equation y = ax + b.
+ */
+ private double getA( int x1, int x2, double z1, double z2 )
+ {
+ return ( z2 - z1 ) / ( double ) ( x2 - x1 );
+ }
+ /**
+ * Determines the constant b of the linear equation y = ax + b given one point P1(x1, y1) and the slope a.
+ *
+ * @param a - the slope a of the linear equation y = ax + b.
+ * @param x1 - x coordinates for the first point.
+ * @param z1 - z coordinates for the first point.
+ * @return the b constant of the linear equation y = ax + b.
+ */
+ private double getB( double a, int x1, double z1 )
+ {
+ return z1 - ( a * x1 );
+ }
- /**
- * Determines the unknown z coordinate of a point P using the linear equation y = ax + b,
- * given its x coordinate and 2 points P1(x1, y1) and P2 (x2, y2).
- *
- * @param x1 - x coordinates for the first point.
- * @param x2 - x coordinates for the second point.
- * @param z1 - z coordinates for the first point.
- * @param z2 - z coordinates for the second point.
- * @param x - the x coordinate of a point with unknown z coordinate.
- * @return * @return - the z coordinate corresponding to the x coordinate.
- */
- private static int executeInt( int x1, int x2, double z1, double z2, int x )
- {
- double a = getA( x1, x2, z1, z2 );
- double b = getB( a, x1, z1 );
- return executeInt( a, b, x );
- }
+ /**
+ * Determines the unknown z coordinate of a point P given its x coordinate,
+ * the slope and the constant of the linear equation y = ax + b.
+ *
+ * @param a - the slope a of the linear equation y = ax + b.
+ * @param b - the b constant of the linear equation y = ax + b.
+ * @param x - the x coordinate of a point with unknown z coordinate.
+ * @return - the z coordinate corresponding to the x coordinate.
+ */
+ private int executeInt( double a, double b, int x )
+ {
+ return ( int ) Math.round( a * x + b );
+ }
- /**
- * Returns an interpolated version of the specified image in the specified dimension.
- *
- * @param zMap the image to interpolate.
- * @param dimension the dimension of the interpolation
- * @return the interpolated image in the specified dimension
- */
- private static Img< UnsignedShortType > execute( Img< UnsignedShortType > zMap, int dimension )
- {
- Img< UnsignedShortType > interpolated = zMap.copy();
- RandomAccess< UnsignedShortType > interpolatedAccess = interpolated.randomAccess();
- RandomAccess< UnsignedShortType > zMapAccess = zMap.randomAccess();
- int secondDimension = Math.abs( dimension - 1 );
- int indexMax = ( int ) zMap.dimension( secondDimension ) - 1;
+ /**
+ * Determines the unknown z coordinate of a point P using the linear equation y = ax + b,
+ * given its x coordinate and 2 points P1(x1, y1) and P2 (x2, y2).
+ *
+ * @param x1 - x coordinates for the first point.
+ * @param x2 - x coordinates for the second point.
+ * @param z1 - z coordinates for the first point.
+ * @param z2 - z coordinates for the second point.
+ * @param x - the x coordinate of a point with unknown z coordinate.
+ * @return * @return - the z coordinate corresponding to the x coordinate.
+ */
+ private int executeInt( int x1, int x2, double z1, double z2, int x )
+ {
+ double a = getA( x1, x2, z1, z2 );
+ double b = getB( a, x1, z1 );
+ return executeInt( a, b, x );
+ }
- for ( int u = 0; u <= zMap.dimension( dimension ) - 1; u++ )
+ /**
+ * Returns an interpolated version of the specified image in the specified dimension.
+ *
+ * @param input the image to interpolate.
+ * @param dimension the dimension of the interpolation
+ * @return the interpolated image in the specified dimension
+ */
+ private Img< UnsignedShortType > execute( RandomAccessibleInterval< UnsignedShortType > input, int dimension )
{
- zMapAccess.setPosition( u, dimension );
- interpolatedAccess.setPosition( u, dimension );
- int X1;
- int X2;
- for ( int v = 0; v <= zMap.dimension( secondDimension ) - 1; v++ )
+ ImgFactory<UnsignedShortType> factory = new ArrayImgFactory<>(new UnsignedShortType());
+ Img< UnsignedShortType > interpolated = factory.create( input );
+ ImgUtil.copy( input, interpolated );
+ RandomAccess< UnsignedShortType > interpolatedAccess = interpolated.randomAccess();
+ RandomAccess< UnsignedShortType > zMapAccess = input.randomAccess();
+ int secondDimension = Math.abs( dimension - 1 );
+ int indexMax = ( int ) input.dimension( secondDimension ) - 1;
+ for ( int u = 0; u <= input.dimension( dimension ) - 1; u++ )
{
+ zMapAccess.setPosition( u, dimension );
+ interpolatedAccess.setPosition( u, dimension );
+ int X1;
+ int X2;
+ for ( int v = 0; v <= input.dimension( secondDimension ) - 1; v++ )
+ {
- zMapAccess.setPosition( v, secondDimension );
+ zMapAccess.setPosition( v, secondDimension );
- interpolatedAccess.setPosition( v, secondDimension );
- if ( zMapAccess.get().getInteger() == 0 )// there no value at this position
- {
- X1 = v - 1;// the previous index.
- if ( X1 >= 0 )
+ interpolatedAccess.setPosition( v, secondDimension );
+ if ( zMapAccess.get().getInteger() == 0 )// there no value at this position
{
- zMapAccess.setPosition( X1, secondDimension );
- int Y1 = zMapAccess.get().copy().getInteger();
- if ( Y1 != 0 )
+ X1 = v - 1;// the previous index.
+ if ( X1 >= 0 )
{
- X2 = searchX2( zMapAccess, v, indexMax, secondDimension );
- if ( X2 < indexMax && X2 - X1 <= 250 ) //an interpolation can only be done for a distance of less or equals to 10 pixels.
+ zMapAccess.setPosition( X1, secondDimension );
+ int Y1 = zMapAccess.get().copy().getInteger();
+ if ( Y1 != 0 )
{
- zMapAccess.setPosition( X2, secondDimension );
- int Y2 = zMapAccess.get().copy().getInteger();
-
- for ( int i = v; i <= X2; i++ )// interpolation between the interval [X1, X2].
+ X2 = searchX2( zMapAccess, v, indexMax, secondDimension );
+ if ( X2 < indexMax && X2 - X1 <= 250 ) //an interpolation can only be done for a distance of less or equals to 10 pixels.
{
- int result = executeInt( X1, X2, Y1, Y2, i );
- interpolatedAccess.setPosition( i, secondDimension );
- interpolatedAccess.get().set( result );
+ zMapAccess.setPosition( X2, secondDimension );
+ int Y2 = zMapAccess.get().copy().getInteger();
+
+ for ( int i = v; i <= X2; i++ )// interpolation between the interval [X1, X2].
+ {
+ int result = executeInt( X1, X2, Y1, Y2, i );
+ interpolatedAccess.setPosition( i, secondDimension );
+ interpolatedAccess.get().set( result );
+ }
}
- }
- v = X2;// we don't need to search in the interval [X1, X2].
+ v = X2;// we don't need to search in the interval [X1, X2].
+ }
}
}
}
}
+ return interpolated;
}
- return interpolated;
- }
- /**
- * Returns an interpolated version of the specified image.
- * The interpolation is the mean of the interpolated image in both dimensions dimension.
- *
- * @param zMap the image to interpolate
- * @return the interpolated resulting image
- */
- public static Img< UnsignedShortType > execute( Img< UnsignedShortType > zMap )
- {
- ImageJFunctions.show( zMap, "zMap" );
- Img< UnsignedShortType > interpolated0 = execute( zMap, 0 );
-// ImageJFunctions.show( interpolated0, "interpolated 0" );
- Img< UnsignedShortType > interpolated1 = execute( zMap, 1 );
-// ImageJFunctions.show( interpolated1, "interpolated 1" );
- Cursor< UnsignedShortType > cursor0 = interpolated0.cursor();
- Cursor< UnsignedShortType > cursor1 = interpolated1.cursor();
-
- while ( cursor0.hasNext() )
+
+ /**
+ * This method returns the first position where the pixel value is different from 0 or the maximum index otherwise.
+ *
+ * @param randomAccess the {@link RandomAccess} of the image to interpolate.
+ * @param x the starting index.
+ * @param max the maximum index value.
+ * @param dim - the dimension to search in.
+ * @return the index at which there is a value > 0 or the maximum index value otherwise.
+ */
+ private int searchX2( RandomAccess< UnsignedShortType > randomAccess, int x, int max, int dim )
{
- cursor0.fwd();
- cursor1.fwd();
- int type0 = cursor0.get().getInteger();
- int type1 = cursor1.get().getInteger();
- if ( type0 != 0 )
+ while ( x + 1 <= max )
{
- if ( type1 != 0 )
+ randomAccess.setPosition( x + 1, dim );
+ if ( randomAccess.get().copy().getInteger() != 0 )
{
- cursor0.get().set( ( type0 + type1 ) / 2 );
+ return x + 1;
}
+ x++;
}
- else if ( type1 != 0 )
- {
- cursor0.get().set( cursor1.get() );
- }
+ return max;
}
- return interpolated0;
- }
- /**
- * This method returns the first position where the pixel value is different from 0 or the maximum index otherwise.
- *
- * @param randomAccess the {@link RandomAccess} of the image to interpolate.
- * @param x the starting index.
- * @param max the maximum index value.
- * @param dim - the dimension to search in.
- * @return the index at which there is a value > 0 or the maximum index value otherwise.
- */
- private static int searchX2( RandomAccess< UnsignedShortType > randomAccess, int x, int max, int dim )
- {
- while ( x + 1 <= max )
+ public Img< UnsignedShortType > getOutput()
{
- randomAccess.setPosition( x + 1, dim );
- if ( randomAccess.get().copy().getInteger() != 0 )
- {
- return x + 1;
- }
- x++;
+ return output;
}
- return max;
}
+
+
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/IsolatedPixFilter.java b/src/main/java/fr/pasteur/ida/zellige/utils/IsolatedPixFilter.java
deleted file mode 100644
index 74507ba399709d9cb1eb7e0e94e9871f8011babb..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/utils/IsolatedPixFilter.java
+++ /dev/null
@@ -1,118 +0,0 @@
-package fr.pasteur.ida.zellige.utils;
-
-
-import net.imglib2.Cursor;
-import net.imglib2.IterableInterval;
-import net.imglib2.RandomAccess;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.algorithm.neighborhood.Neighborhood;
-import net.imglib2.algorithm.neighborhood.RectangleShape;
-import net.imglib2.algorithm.neighborhood.RectangleShape.NeighborhoodsAccessible;
-import net.imglib2.img.Img;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.view.IntervalView;
-import net.imglib2.view.Views;
-
-import static net.imglib2.util.ImgUtil.copy;
-
-
-//TODO Javadoc
-/**
- *
- * @author Céline Trébeau - 2020
- */
-
-public class IsolatedPixFilter {
-
- public static <T extends RealType<T> & NativeType<T>>Img<T> run(final Img<T> source, int radius, int iter, int n){
- IsolatedPixOperator <T> isolatedPixOperator = new IsolatedPixOperator<>(source,radius, iter, n);
- isolatedPixOperator.process();
- return isolatedPixOperator.getResult();
-
- }
-
- private static class IsolatedPixOperator<T extends RealType<T> & NativeType<T>> {
-
- private final Img<T> source;
-
- private final Img<T> output;
-
- private final int iter;
-
- private final int radius;
-
- private final int n;
-
-
- /**
- * Instantiate a new median filter that will operate on the specified
- * source.
- *
- * @param source the source to operate on.
- */
- public IsolatedPixOperator(final Img<T> source,int radius, int iter, int n) {
- this.source = source;
- this.output = source.copy();
- this.radius = radius;
- this.iter = iter;
- this.n = n;
-
- }
-
- public void process() {
-
- Img<T> temp = source.factory().create(source);//TODO may be 2 different neighbour number to reduce the iteration
- copy(source, temp);
-
- for (int i = 0; i <= iter - 1; i++) {
- process(temp, output,radius, n);
- temp = output.copy();
-// ImageJFunctions.show( output, "iteration "+ i );
- }
- }
-
- public void process(Img<T> source, Img<T> output,int radius, int n) {
- for (long z = 0; z < source.dimension(2); z++) {//TODO why use long ?
- final IntervalView<T> slice = Views.hyperSlice(source, 2, z);
- final IntervalView<T> outputSlice = Views.hyperSlice(output, 2, z);
- processSlice(slice, outputSlice, radius, n);
-
- }
-// System.out.println("-------------------------" );
- }
-
-
- private void processSlice(final RandomAccessibleInterval<T> in, final IterableInterval<T> out,int radius, int n) {
- final Cursor<T> cursor = out.cursor();
- final RectangleShape shape = new RectangleShape(radius, true);
- final NeighborhoodsAccessible<T> accessible = shape.neighborhoodsRandomAccessible(Views.extendZero(in));
- final RandomAccess<Neighborhood<T>> nra = accessible.randomAccess(in);
- int count = 0;
- while (cursor.hasNext()) {
- int values = 0;
- cursor.fwd();
- if (cursor.get().getRealFloat() != 0)
- {
- nra.setPosition(cursor);
- for (final T pixel : nra.get()) {
- if (pixel.getRealFloat() > 0) {
- values++;
- }
- }
- if (values < n) {
- cursor.get().setReal(0);
- count++;
- }
- }
- }
-// System.out.println(count + " pixels removed");
- }
-
-
- public Img<T> getResult() {
- return output;
- }
-
- }
-}
\ No newline at end of file
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/LocalExtremaDetection.java b/src/main/java/fr/pasteur/ida/zellige/utils/LocalExtremaDetection.java
new file mode 100644
index 0000000000000000000000000000000000000000..7bd2c3d0d45d511c3dcdba8a59ec5ca022f20e37
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/LocalExtremaDetection.java
@@ -0,0 +1,154 @@
+package fr.pasteur.ida.zellige.utils;
+
+import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
+import net.imglib2.RandomAccess;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.img.Img;
+import net.imglib2.img.ImgFactory;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+import net.imglib2.view.IntervalView;
+import net.imglib2.view.Views;
+
+public class LocalExtremaDetection
+{
+
+
+ public static < T extends RealType< T > & NativeType< T > > Img< T > findMinima( RandomAccessibleInterval< T > input,
+ ImgFactory< T > factory )
+ {
+ Img< T > minima = factory.create( input.dimension( 0 ), input.dimension( 1 ), input.dimension( 2 ) );
+ new LocalExtremaDetectionOperator<>( input, factory, minima, "min" );
+ return minima;
+ }
+
+
+ public static < T extends RealType< T > & NativeType< T > > Img< T > findMaxima( RandomAccessibleInterval< T > input,
+ ImgFactory< T > factory )
+ {
+ Img< T > maxima = factory.create( input.dimension( 0 ), input.dimension( 1 ), input.dimension( 2 ) );
+ new LocalExtremaDetectionOperator<>( input, factory, maxima, "max" );
+ return maxima;
+ }
+
+ private static class LocalExtremaDetectionOperator< T extends RealType< T > & NativeType< T > >
+ {
+
+ private final RandomAccessibleInterval< T > input;
+ private final ImgFactory< T > factory;
+ private final RandomAccessibleInterval< T > output;
+ private final String type;
+
+ public LocalExtremaDetectionOperator( RandomAccessibleInterval< T > input, ImgFactory< T > factory,
+ RandomAccessibleInterval< T > output, String type )
+ {
+ this.input = input;
+ this.factory = factory;
+ this.output = output;
+ this.type = type;
+ findExtrema();
+ }
+
+ /**
+ * Finds all the local extrema of an input stack image,
+ * according to given local and global thresholds by first using a gaussian blur.
+ * The local maximums are stored in a 2D {@link Pixels} array.
+ */
+ private void
+ findExtrema()
+ {
+ // For each individual orthogonal XZ sections.*/
+ for ( int x = 0; x <= input.dimension( 0 ) - 1; x++ )// iteration on dimension X
+ {
+ try
+ {
+ // The YZ section.
+ IntervalView< T > intervalView = Views.hyperSlice( this.input, 0, x );
+ // Each maximum found is stored in double Pixel array .
+ getExtrema( intervalView, x );
+ }
+ catch ( Exception e )
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+
+
+ /**
+ * Finds all the local maximums of an 2D image,
+ * according to given local and global thresholds by first using a gaussian blur and then a partial derivative
+ * The local maximums are stored in a 2D {@link Pixels} array.
+ *
+ * @param YZProjection - An orthogonal section (2 dimensions).
+ * @param x - the index of the orthogonal section AKA the stack index in dimension X.
+ */
+ private void
+ getExtrema( RandomAccessibleInterval< T > YZProjection, int x )
+ {
+ // Output for partial derivative.
+ // Addition of one supplementary line, in case the last slice contains some local maximums
+ RandomAccessibleInterval< T > partialDerivative = factory.create( YZProjection.dimension( 0 ) + 1,
+ YZProjection.dimension( 1 ) + 1 );
+ // Partial derivative computation */
+ Utils.derivative( YZProjection, partialDerivative );
+ getExtrema( partialDerivative, YZProjection, x );
+ }
+
+
+ /**
+ * @param partialDerivative the x-positioned partial derivative section of the input image as a {@link RandomAccessibleInterval}
+ * @param x the index in dimension X
+ */
+ private void
+ getExtrema
+ ( RandomAccessibleInterval< T > partialDerivative, RandomAccessibleInterval< T > original, int x )
+ {
+ RandomAccess< T > derivativeAccess = partialDerivative.randomAccess();
+ RandomAccess< T > maxAccess = output.randomAccess();
+ RandomAccess< T > oriAccess = original.randomAccess();
+
+ for ( int y = 0; y <= output.dimension( 1 ) - 1; y++ )
+ {
+ derivativeAccess.setPosition( y, 0 );
+ for ( int z = 0; z <= output.dimension( 2 ) - 1; z++ )
+ {
+ if ( isALocalExtrema( derivativeAccess, z ) )
+ {
+ Utils.setPosition( oriAccess, y, z );
+ Utils.setPosition( maxAccess, x, y, z );
+ maxAccess.get().set( oriAccess.get() );
+ }
+ }
+ }
+ }
+
+
+ /**
+ * Method to find if a pixel of a given stack is a local maximum.
+ * <p>
+ * (X or Y for respectively XZ sections and YZ sections).
+ *
+ * @param derivative - the first {@link RandomAccess} for the partial derivative image
+ * set at index v for dimension 0.
+ * @param z - the index of the Z dimension
+ * @return - true if the position (v, z) is a local maximum false otherwise.
+ */
+ private boolean isALocalExtrema( RandomAccess< T > derivative, int z ) //throws Exception
+ {
+ derivative.setPosition( z, 1 );
+ final double tZero = derivative.get().getRealDouble();
+ derivative.setPosition( ( z + 1 ), 1 );
+ final double tOne = derivative.get().getRealDouble();
+ if ( type.equals( "max" ) )
+ {
+ return ( tZero >= 0 && tOne < 0 );
+ }
+ else
+ {
+ return ( tZero < 0 && tOne >= 0 );
+ }
+ }
+
+ }
+}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/LocalMaximumDetection.java b/src/main/java/fr/pasteur/ida/zellige/utils/LocalMaximumDetection.java
deleted file mode 100644
index b40c774a40377c2fb20776500641c127b5bd8fdf..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/utils/LocalMaximumDetection.java
+++ /dev/null
@@ -1,174 +0,0 @@
-package fr.pasteur.ida.zellige.utils;
-
-
-import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
-import net.imglib2.RandomAccess;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.img.Img;
-import net.imglib2.img.ImgFactory;
-import net.imglib2.img.display.imagej.ImageJFunctions;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.view.IntervalView;
-import net.imglib2.view.Views;
-
-
-/**
- * @author ctrebeau
- * This class is used to select local maximums of a stack image (3 dimensions) by using the static method
- * findMaximums().
- * First a gaussian convolution (anisotropic ) is performed then for each orthogonal section (XZ section)
- * the local maximums are found by the determination of the partial derivative in the section first dimension
- * AKA dimension Y.
- */
-
-public class LocalMaximumDetection
-{
-
- /**
- * Finds all the local maximums of an input stack image,
- * according to given local and global thresholds by first using a gaussian blur.
- * The local maximums are stored in a 2D {@link Pixels} array.
- *
- * @param zStack - the z-stack to analysed.
- * @param <T> - the type of the z-stack.
- */
-
-
- public static < T extends RealType< T > & NativeType< T > > Img< T >
- findMaximums( RandomAccessibleInterval< T > zStack, ImgFactory< T > factory )
- {
-// Img< T > maximums = factory.create( zStack );
- Img< T > maximums = factory.create( zStack.dimension( 0 ), zStack.dimension( 1 ), zStack.dimension( 2 ) );
-
- // For each individual orthogonal XZ sections.*/
- for ( int x = 0; x <= zStack.dimension( 0 ) - 1; x++ )// iteration on dimension X
- {
- try
- {
- // The YZ section.
- IntervalView< T > intervalView = Views.hyperSlice( zStack, 0, x );
- // Each maximum found is stored in double Pixel array .
- findListOfMaximums( intervalView, factory, x, maximums );
- }
- catch ( Exception e )
- {
- e.printStackTrace();
- }
- }
- return maximums;
- }
-
-
- /**
- * Finds all the local maximums of an 2D image,
- * according to given local and global thresholds by first using a gaussian blur and then a partial derivative
- * The local maximums are stored in a 2D {@link Pixels} array.
- *
- * @param YZProjection - An orthogonal section (2 dimensions).
- * @param x - the index of the orthogonal section AKA the stack index in dimension X.
- * @param <T> - the YZProjection type.
- */
- private static < T extends RealType< T > & NativeType< T > > void
- findListOfMaximums( RandomAccessibleInterval< T > YZProjection, ImgFactory< T > factory, int x,
- RandomAccessibleInterval< T > maximums )
- {
-
- // Output for partial derivative.
- // Addition of one supplementary line, in case the last slice contains some local maximums
- RandomAccessibleInterval< T > partialDerivative = factory.create( YZProjection.dimension( 0 ) + 1,
- YZProjection.dimension( 1 ) + 1 );
- // Partial derivative computation */
- Utils.derivative( YZProjection, partialDerivative );
- getListOfLocalMaximum( maximums, partialDerivative,YZProjection, x );
- }
-
-
- /**
- * @param max the output image containing the local maximums as a {@link RandomAccessibleInterval}
- * @param partialDerivative the x-positioned partial derivative section of the input image as a {@link RandomAccessibleInterval}
- * @param x the index in dimension X
- * @param <T> the type of both {@link RandomAccessibleInterval}
- */
- private static < T extends RealType< T > & NativeType< T > > void
- getListOfLocalMaximum
- ( RandomAccessibleInterval< T > max,
- RandomAccessibleInterval< T > partialDerivative,
- int x
- )
- {
- RandomAccess< T > derivativeAccess = partialDerivative.randomAccess();
- RandomAccess< T > maxAccess = max.randomAccess();
-
- for ( int y = 0; y <= max.dimension( 1 ) - 1; y++ )
- {
- derivativeAccess.setPosition( y, 0 );
- for ( int z = 0; z <= max.dimension( 2 ) - 1; z++ )
- {
- if ( isALocalMaximum( derivativeAccess, z ) )
- {
- Utils.setPosition( maxAccess, x, y, z );
- maxAccess.get().setOne();
- }
- }
- }
- }
-
- private static < T extends RealType< T > & NativeType< T > > void
- getListOfLocalMaximum
- ( RandomAccessibleInterval< T > notMax,
- RandomAccessibleInterval< T > partialDerivative,
- RandomAccessibleInterval <T> original,
- int x
- )
- {
- RandomAccess< T > derivativeAccess = partialDerivative.randomAccess();
- RandomAccess< T > maxAccess = notMax.randomAccess();
- RandomAccess< T > oriAccess = original.randomAccess();
-
- for ( int y = 0; y <= notMax.dimension( 1 ) - 1; y++ )
- {
- derivativeAccess.setPosition( y, 0 );
- for ( int z = 0; z <= notMax.dimension( 2 ) - 1; z++ )
- {
- if ( isALocalMaximum( derivativeAccess, z ) )
- {
- Utils.setPosition( oriAccess, y, z );
- Utils.setPosition( maxAccess, x, y, z );
- maxAccess.get().set( oriAccess.get() );
-// maxAccess.get().setOne();
- }
- }
- }
- }
-
- /**
- * Method to find if a pixel of a given stack is a local maximum.
- * <p>
- * (X or Y for respectively XZ sections and YZ sections).
- *
- * @param derivative - the first {@link RandomAccess} for the partial derivative image
- * set at index v for dimension 0.
- * @param z - the index of the Z dimension
- * @param <T> - the type of the image
- * @return - true if the position (v, z) is a local maximum false otherwise.
- */
- private static < T extends RealType< T > & NativeType< T > > boolean isALocalMaximum
- ( RandomAccess< T > derivative, int z )
- {
- derivative.setPosition( z, 1 );
- final double tZero = derivative.get().getRealDouble();
- derivative.setPosition( ( z + 1 ), 1 );
- final double tOne = derivative.get().getRealDouble();
- return ( tZero >= 0 && tOne < 0 );
- }
- private static < T extends RealType< T > & NativeType< T > > boolean isALocalMinimum
- ( RandomAccess< T > derivative, int z )
- {
- derivative.setPosition( z, 1 );
- final double tZero = derivative.get().getRealDouble();
- derivative.setPosition( ( z + 1 ), 1 );
- final double tOne = derivative.get().getRealDouble();
- return ( tZero <0 && tOne >= 0 );
- }
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/LocalMinimumDetection.java b/src/main/java/fr/pasteur/ida/zellige/utils/LocalMinimumDetection.java
deleted file mode 100644
index f54f264769c5bfa141305e0a7854ad12376f6664..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/utils/LocalMinimumDetection.java
+++ /dev/null
@@ -1,173 +0,0 @@
-package fr.pasteur.ida.zellige.utils;
-
-
-import fr.pasteur.ida.zellige.surfaceConstruction.element.Pixels;
-import net.imglib2.RandomAccess;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.img.Img;
-import net.imglib2.img.ImgFactory;
-import net.imglib2.img.display.imagej.ImageJFunctions;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.util.ImgUtil;
-import net.imglib2.view.IntervalView;
-import net.imglib2.view.Views;
-
-
-/**
- * @author ctrebeau
- * This class is used to select local maximums of a stack image (3 dimensions) by using the static method
- * findMaximums().
- * First a gaussian convolution (anisotropic ) is performed then for each orthogonal section (XZ section)
- * the local maximums are found by the determination of the partial derivative in the section first dimension
- * AKA dimension Y.
- */
-
-public class LocalMinimumDetection
-{
-
- /**
- * Finds all the local maximums of an input stack image,
- * according to given local and global thresholds by first using a gaussian blur.
- * The local maximums are stored in a 2D {@link Pixels} array.
- *
- * @param zStack - the z-stack to analysed.
- * @param <T> - the type of the z-stack.
- */
-
-
- public static < T extends RealType< T > & NativeType< T > > Img< T >
- findMinimums( RandomAccessibleInterval< T > zStack, ImgFactory< T > factory )
- {
- Img< T > minimums = factory.create( zStack.dimension( 0 ), zStack.dimension( 1 ), zStack.dimension( 2 ) );
-// ImgUtil.copy( zStack, minimums );
- // For each individual orthogonal XZ sections.*/
- for ( int x = 0; x <= zStack.dimension( 0 ) - 1; x++ )// iteration on dimension X
- {
- try
- {
- // The YZ section.
- IntervalView< T > intervalView = Views.hyperSlice( zStack, 0, x );
-// if (x == 15)
-// {
-// ImageJFunctions.show(intervalView);
-// }
- // Each maximum found is stored in double Pixel array .
- findListOfMinimum( intervalView, factory, x, minimums );
- }
- catch ( Exception e )
- {
- e.printStackTrace();
- }
- }
- return minimums;
- }
-
-
- /**
- * Finds all the local maximums of an 2D image,
- * according to given local and global thresholds by first using a gaussian blur and then a partial derivative
- * The local maximums are stored in a 2D {@link Pixels} array.
- *
- * @param YZProjection - An orthogonal section (2 dimensions).
- * @param x - the index of the orthogonal section AKA the stack index in dimension X.
- * @param <T> - the YZProjection type.
- */
- private static < T extends RealType< T > & NativeType< T > > void
- findListOfMinimum( RandomAccessibleInterval< T > YZProjection, ImgFactory< T > factory, int x,
- RandomAccessibleInterval< T > maximums )
- {
- // Output for partial derivative.
- // Addition of one supplementary line, in case the last slice contains some local maximums
- RandomAccessibleInterval< T > partialDerivative = factory.create( YZProjection.dimension( 0 ) + 1,
- YZProjection.dimension( 1 ) + 1 );
- // Partial derivative computation */
- Utils.derivative( YZProjection, partialDerivative );
-// if (x == 15)
-// {
-// ImageJFunctions.show(partialDerivative);
-// }
- getListOfLocalMinimum( maximums, partialDerivative,YZProjection, x );
- }
-
-
- /**
- * @param max the output image containing the local maximums as a {@link RandomAccessibleInterval}
- * @param partialDerivative the x-positioned partial derivative section of the input image as a {@link RandomAccessibleInterval}
- * @param x the index in dimension X
- * @param <T> the type of both {@link RandomAccessibleInterval}
- */
- private static < T extends RealType< T > & NativeType< T > > void
- getListOfLocalMinimum
- ( RandomAccessibleInterval< T > max,
- RandomAccessibleInterval< T > partialDerivative,
- int x
- )
- {
- RandomAccess< T > derivativeAccess = partialDerivative.randomAccess();
- RandomAccess< T > maxAccess = max.randomAccess();
-
- for ( int y = 0; y <= max.dimension( 1 ) - 1; y++ )
- {
- derivativeAccess.setPosition( y, 0 );
- for ( int z = 0; z <= max.dimension( 2 ) - 1; z++ )
- {
- if ( isALocalMinimum( derivativeAccess, z ) )
- {
- Utils.setPosition( maxAccess, x, y, z );
- maxAccess.get().setOne();
- }
- }
- }
- }
-
- private static < T extends RealType< T > & NativeType< T > > void
- getListOfLocalMinimum
- ( RandomAccessibleInterval< T > minimums,
- RandomAccessibleInterval< T > partialDerivative,
- RandomAccessibleInterval <T> original,
- int x
- )
- {
- RandomAccess< T > derivativeAccess = partialDerivative.randomAccess();
- RandomAccess< T > minAccess = minimums.randomAccess();
- RandomAccess< T > oriAccess = original.randomAccess();
-
- for ( int y = 0; y <= minimums.dimension( 1 ) - 1; y++ )
- {
- derivativeAccess.setPosition( y, 0 );
- for ( int z = 0; z <= minimums.dimension( 2 ) - 1; z++ )
- {
- if ( isALocalMinimum( derivativeAccess, z ) )
- {
- Utils.setPosition( oriAccess, y, z );
- Utils.setPosition( minAccess, x, y, z );
- minAccess.get().set( oriAccess.get() );
-// maxAccess.get().setOne();
- }
- }
- }
- }
-
- /**
- * Method to find if a pixel of a given stack is a local maximum.
- * <p>
- * (X or Y for respectively XZ sections and YZ sections).
- *
- * @param derivative - the first {@link RandomAccess} for the partial derivative image
- * set at index v for dimension 0.
- * @param z - the index of the Z dimension
- * @param <T> - the type of the image
- * @return - true if the position (v, z) is a local maximum false otherwise.
- */
-
- private static < T extends RealType< T > & NativeType< T > > boolean isALocalMinimum
- ( RandomAccess< T > derivative, int z )
- {
- derivative.setPosition( z, 1 );
- final double tZero = derivative.get().getRealDouble();
- derivative.setPosition( ( z + 1 ), 1 );
- final double tOne = derivative.get().getRealDouble();
- return ( tZero <0 && tOne >= 0 );
- }
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/LocalOtsuTest.java b/src/main/java/fr/pasteur/ida/zellige/utils/LocalOtsuTest.java
deleted file mode 100644
index f7dfb8ae099f3eb1f845930a7cec25c46089ac90..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/utils/LocalOtsuTest.java
+++ /dev/null
@@ -1,26 +0,0 @@
-package fr.pasteur.ida.zellige.utils;
-
-import net.imglib2.Interval;
-import net.imglib2.algorithm.util.Grids;
-
-import java.util.List;
-
-
-
-class LocalOtsuTest
-{
-
-
- public void grid()
- {
- List< Interval > intervals = Grids.collectAllContainedIntervals( new long[]{ 300, 420, 20 },
- new int[]{ 100, 100, 30} );
- System.out.println("youhou");
- }
-
- public static void main( String[] args )
- {
- LocalOtsuTest l = new LocalOtsuTest();
- l.grid();
- }
-}
\ No newline at end of file
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/MaximumAmplitudeClassification.java b/src/main/java/fr/pasteur/ida/zellige/utils/MaximumAmplitudeClassification.java
index bb15d9423c986d0e0fd71cf42bd76a12adf4e5a5..88314c5a9b614b19cfbde095b8204463d0c1b1e8 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/MaximumAmplitudeClassification.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/MaximumAmplitudeClassification.java
@@ -1,6 +1,5 @@
package fr.pasteur.ida.zellige.utils;
-import fr.pasteur.ida.zellige.surfaceConstruction.construction.SurfacesExtraction;
import net.imglib2.Cursor;
import net.imglib2.Interval;
import net.imglib2.RandomAccess;
@@ -173,9 +172,11 @@ public class MaximumAmplitudeClassification
public void run()
{
- Img< T > maximums = LocalMaximumDetection.findMaximums( input, factory );
- Img< T > minimums = LocalMinimumDetection.findMinimums( input, factory );
- Img< T > amp = getAmplitude( maximums, factory, minimums );
+// Img< T > maximums = LocalMaximumDetection.findMaximums( input, factory );
+ Img< T > maximums = LocalExtremaDetection.findMaxima( input, factory );
+// Img< T > minimums = LocalMinimumDetection.findMinimums( input, factory );
+ Img< T > minimums = LocalExtremaDetection.findMinima( input, factory );
+ Img< T > amp = getAmplitude( maximums, factory, minimums );
T TMax = Threshold.getFirstMaxValue( maximums, false );
TMax.mul( amplitudeThreshold );
this.amplitude = Thresholder.threshold( amp.copy(), TMax, true, 2 );
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/MaximumVarianceFilter.java b/src/main/java/fr/pasteur/ida/zellige/utils/MaximumVarianceFilter.java
deleted file mode 100644
index 8aaededdeae158de75c3cfaae42df59742739b11..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/utils/MaximumVarianceFilter.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package fr.pasteur.ida.zellige.utils;
-
-import net.imglib2.Cursor;
-import net.imglib2.img.Img;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-
-public class MaximumVarianceFilter <T extends RealType<T> & NativeType<T>>
-{
-
- private final Img<T> variance;
-
- private final Img<T> max;
- private Img<T> output;
-
- public MaximumVarianceFilter(Img <T> max, final Img<T> variance) {
- this.max = max;
- this.variance = variance;
- this.output = variance.factory().create(variance.dimension(0), variance.dimension(1), variance.dimension(2));
-// copy(max, output);
- }
-
- public void process() {
-
-
- Cursor<T> varCursor = variance.cursor();
- Cursor<T> maxCursor = max.cursor();
- Cursor<T> outCursor = output.cursor();
- while (varCursor.hasNext())
- {
- varCursor.fwd();
- maxCursor.fwd();
- outCursor.fwd();
- final double var = varCursor.get().getRealDouble();
- final double m = maxCursor.get().getRealDouble();
- if (m!= 0 && var != 0)
-
- {
- outCursor.get().setReal(1);
- }
- }
-
- output = IsolatedPixFilter.run(output.copy(),1, 5, 2);
-
- }
-
-
- public Img<T> getResult() {
- return output;
- }
-
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/MedianSkipZeros.java b/src/main/java/fr/pasteur/ida/zellige/utils/MedianSkipZeros.java
deleted file mode 100644
index 1c5bd8eba7930c69255b8dd5b67e1aff1080ab58..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/utils/MedianSkipZeros.java
+++ /dev/null
@@ -1,197 +0,0 @@
-package fr.pasteur.ida.zellige.utils;
-
-import java.util.Arrays;
-import java.util.List;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.stream.Collectors;
-
-import ij.IJ;
-import ij.ImagePlus;
-import net.imagej.ImageJ;
-import net.imglib2.Cursor;
-import net.imglib2.Interval;
-import net.imglib2.RandomAccess;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.algorithm.neighborhood.Neighborhood;
-import net.imglib2.algorithm.neighborhood.RectangleShape;
-import net.imglib2.algorithm.neighborhood.RectangleShape.NeighborhoodsAccessible;
-import net.imglib2.img.Img;
-import net.imglib2.img.ImgFactory;
-import net.imglib2.img.display.imagej.ImageJFunctions;
-import net.imglib2.loops.IntervalChunks;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.util.Util;
-import net.imglib2.view.IntervalView;
-import net.imglib2.view.Views;
-
-public class MedianSkipZeros
-{
-
- /**
- * Apply a 3x3 median to a nD image, possibly skipping for pixel with
- * 0-values. The computation is multithreaded.
- *
- * @param <T>
- * the pixel type of the source image.
- * @param source
- * the source image.
- * @param skipZeros
- * if <code>true</code>, pixels with 0-value will be skipped.
- * @return a new image of the same pixel type that of the source.
- */
- public static final < T extends RealType< T > & NativeType< T > > Img< T > median( final RandomAccessibleInterval< T > source, final boolean skipZeros )
- {
- // Prepare output.
- final ImgFactory< T > factory = Util.getArrayOrCellImgFactory( source, Util.getTypeFromInterval( source ) );
- final Img< T > output = factory.create( source );
-
- // Create the neighborhoods.
- final RectangleShape kernel = new RectangleShape( 1, false );
- final NeighborhoodsAccessible< T > neighborhoods = kernel.neighborhoodsRandomAccessible( Views.extendMirrorDouble( source ) );
-
- // Divide into chunks.
- final int numberOfChunks = Runtime.getRuntime().availableProcessors() / 2; // Only one proc
- final List< Interval > chunks = IntervalChunks.chunkInterval( source, numberOfChunks );
-
- // Create tasks.
- final List< Runnable > runnables = ( skipZeros )
- ? chunks.stream()
- .map( chunk -> new MedianOperatorSkipZeros<>( chunk, output, source, neighborhoods ) )
- .collect( Collectors.toList() )
- : chunks.stream()
- .map( chunk -> new MedianOperator<>( chunk, output, source, neighborhoods ) )
- .collect( Collectors.toList() );
-
- // Launch computation on several threads
- final ExecutorService executorService = Executors.newFixedThreadPool( numberOfChunks );
- runnables.forEach( executorService::submit );
- executorService.shutdown();
-
- return output;
- }
-
- private static final class MedianOperator< T extends RealType< T > & NativeType< T > > implements Runnable
- {
-
- private final Interval chunk;
-
- private final Img< T > output;
-
- private final RandomAccessibleInterval< T > source;
-
- private final NeighborhoodsAccessible< T > neighborhoods;
-
- private MedianOperator( final Interval chunk, final Img< T > output, final RandomAccessibleInterval< T > source, final NeighborhoodsAccessible< T > neighborhoods )
- {
- this.chunk = chunk;
- this.output = output;
- this.source = source;
- this.neighborhoods = neighborhoods;
- }
-
- @Override
- public void run()
- {
- final IntervalView< T > interval = Views.interval( source, chunk );
-
- final Cursor< T > sourceCursor = interval.localizingCursor();
- final RandomAccess< T > raOutput = output.randomAccess( chunk );
- final RandomAccess< Neighborhood< T > > raNeighborhoods = neighborhoods.randomAccess( chunk );
-
- final int size = ( int ) raNeighborhoods.get().size();
- final double[] values = new double[ size ];
-
- while ( sourceCursor.hasNext() )
- {
- sourceCursor.fwd();
-
- raNeighborhoods.setPosition( sourceCursor );
- int index = 0;
- for ( final T pixel : raNeighborhoods.get() )
- values[ index++ ] = pixel.getRealDouble();
-
- Arrays.sort( values, 0, index );
- final double median = values[ ( index - 1 ) / 2 ];
-
- raOutput.setPosition( sourceCursor );
- raOutput.get().setReal( median );
- }
- }
- }
-
- private static final class MedianOperatorSkipZeros< T extends RealType< T > & NativeType< T > > implements Runnable
- {
-
- private final Interval chunk;
-
- private final Img< T > output;
-
- private final RandomAccessibleInterval< T > source;
-
- private final NeighborhoodsAccessible< T > neighborhoods;
-
- private MedianOperatorSkipZeros( final Interval chunk, final Img< T > output, final RandomAccessibleInterval< T > source, final NeighborhoodsAccessible< T > neighborhoods )
- {
- this.chunk = chunk;
- this.output = output;
- this.source = source;
- this.neighborhoods = neighborhoods;
- }
-
- @Override
- public void run()
- {
- final IntervalView< T > interval = Views.interval( source, chunk );
-
- final Cursor< T > sourceCursor = interval.localizingCursor();
- final RandomAccess< T > raOutput = output.randomAccess( chunk );
- final RandomAccess< Neighborhood< T > > raNeighborhoods = neighborhoods.randomAccess( chunk );
-
- final int size = ( int ) raNeighborhoods.get().size();
- final double[] values = new double[ size ];
-
- while ( sourceCursor.hasNext() )
- {
- sourceCursor.fwd();
- if ( sourceCursor.get().getRealDouble() == 0 )
- {
- raOutput.setPosition( sourceCursor );
- raOutput.get().set( sourceCursor.get() );
- continue;
- }
-
- raNeighborhoods.setPosition( sourceCursor );
- int index = 0;
- for ( final T pixel : raNeighborhoods.get() )
- values[ index++ ] = pixel.getRealDouble();
-
- Arrays.sort( values, 0, index );
- final double median = values[ ( index - 1 ) / 2 ];
-
- raOutput.setPosition( sourceCursor );
- raOutput.get().setReal( median );
- }
- }
- }
-
- /*
- * DEMO
- */
-
- public static < T extends RealType< T > & NativeType< T > > void main( final String[] args )
- {
- final ImageJ ij = new ImageJ();
- ij.launch( args );
-
- final String imgFile = "doc/STK.tif";
- final ImagePlus imp = IJ.openImage( imgFile );
- imp.show();
-
- final Img< T > wrap = ImageJFunctions.wrap( imp );
- final Img< T > output = MedianSkipZeros.median( wrap, true );
- ImageJFunctions.show( output, "Median skip 0" );
-
- }
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/Otsu.java b/src/main/java/fr/pasteur/ida/zellige/utils/Otsu.java
index c1032b1f0418513fbc7f9b2b4597f0c6c7632044..ef76fce22980e707c314ca731c76d7821383a74f 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/Otsu.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/Otsu.java
@@ -11,9 +11,9 @@ import java.util.TreeMap;
public class Otsu
{
- public static < T extends RealType< T > & NativeType< T > > T getThreshold( IterableInterval< T > source)
+ public static < T extends RealType< T > & NativeType< T > > T getThreshold( IterableInterval< T > source )
{
- OtsuOperator<T> otsuOperator = new OtsuOperator<>( source );
+ OtsuOperator< T > otsuOperator = new OtsuOperator<>( source );
otsuOperator.process();
T threshold = source.firstElement().createVariable();
threshold.setReal( otsuOperator.getThreshold() );
@@ -61,8 +61,7 @@ public class Otsu
for ( int i = 0; i <= n0.length - 1; i++ )
{
-
- output[ i ] = (double) n0[i] / ( double ) N;
+ output[ i ] = ( double ) n0[ i ] / ( double ) N;
}
return output;
}
@@ -73,7 +72,7 @@ public class Otsu
double[] output = new double[ M0.length ];
for ( int i = 0; i <= M0.length - 1; i++ )
{
- output[ i ] = M0[ i ] / n0[ i ] ;
+ output[ i ] = M0[ i ] / n0[ i ];
}
return output;
}
@@ -83,30 +82,30 @@ public class Otsu
double[] output = new double[ M0.length ];
for ( int i = 0; i <= M0.length - 1; i++ )
{
- output[ i ] = (N * mTot - M0[ i ]) / (N-n0[ i ]) ;
+ output[ i ] = ( N * mTot - M0[ i ] ) / ( N - n0[ i ] );
}
return output;
}
- public static double[] getVB( double mTot, double[] m0, double [] m1 , double [] p0, double [] p1)
+ public static double[] getVB( double mTot, double[] m0, double[] m1, double[] p0, double[] p1 )
{
double[] vb = new double[ m0.length ];
for ( int i = 0; i <= m0.length - 1; i++ )
{
- vb[ i ] = p0[i] * Math.pow( (m0[i] - mTot), 2) + p1[i] * Math.pow((m1[i] - mTot), 2);
+ vb[ i ] = p0[ i ] * Math.pow( ( m0[ i ] - mTot ), 2 ) + p1[ i ] * Math.pow( ( m1[ i ] - mTot ), 2 );
}
return vb;
}
- public static int findKMax(double [] vb)
+ public static int findKMax( double[] vb )
{
double max = 0;
int k = 0;
- for(int i = 0 ; i<= vb.length - 1; i ++)
+ for ( int i = 0; i <= vb.length - 1; i++ )
{
- if (vb[i] > max)
+ if ( vb[ i ] > max )
{
- max = vb[i];
+ max = vb[ i ];
k = i;
}
}
@@ -114,13 +113,12 @@ public class Otsu
}
-
- public static double[] getP1( double [] p0)
+ public static double[] getP1( double[] p0 )
{
double[] p1 = new double[ p0.length ];
for ( int i = 0; i <= p0.length - 1; i++ )
{
- p1[ i ] = 1 - p0[i];
+ p1[ i ] = 1 - p0[ i ];
}
return p1;
}
@@ -133,8 +131,8 @@ public class Otsu
while ( cursor.hasNext() )
{
cursor.fwd();
- final double value = cursor.get().getRealDouble();
- Integer j = hm.get(value );
+ final double value = cursor.get().getRealDouble();
+ Integer j = hm.get( value );
hm.put( value, ( j == null ) ? 1 : j + 1 );
}
@@ -159,22 +157,22 @@ public class Otsu
// Setting of mean and number of pixels
int N = 1;
- for(int d = 0 ; d<= source.numDimensions() - 1; d ++)
+ for ( int d = 0; d <= source.numDimensions() - 1; d++ )
{
- N = N* (int) source.dimension( d );
+ N = N * ( int ) source.dimension( d );
}
double mTot = sum / N;
// Cumulative arrays
int[] n0 = makeCumulativeSum( histogram );
double[] M0 = makeCumulativeWeightedSum( histogram, intensities );
- double [] m0 = getLittleM0( M0, n0 );
- double [] p0 = getP0( n0, N );
- double [] m1 = getM1( N, mTot, M0, n0 );
- double [] p1 = getP1( p0 );
- double[] vb = getVB( mTot, m0, m1, p0, p1 );
+ double[] m0 = getLittleM0( M0, n0 );
+ double[] p0 = getP0( n0, N );
+ double[] m1 = getM1( N, mTot, M0, n0 );
+ double[] p1 = getP1( p0 );
+ double[] vb = getVB( mTot, m0, m1, p0, p1 );
int k = findKMax( vb );
- threshold = intensities[k];
+ threshold = intensities[ k ];
}
@@ -184,10 +182,10 @@ public class Otsu
return threshold;
}
- public double sum(double [] array)
+ public double sum( double[] array )
{
double sum = 0;
- for (double d : array )
+ for ( double d : array )
{
sum = d + sum;
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/StackProjection.java b/src/main/java/fr/pasteur/ida/zellige/utils/StackProjection.java
index de605624d3050b6c4a99ae92d9c36c1182b9a0ce..5128dd0992434473847959b1900d32cae3e28f3e 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/StackProjection.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/StackProjection.java
@@ -78,7 +78,7 @@ public class StackProjection
* @param <T>
* @return
*/
- public static < T extends RealType< T > & NativeType< T > > Img< UnsignedShortType > getHeightMap
+ public static < T extends RealType< T > & NativeType< T > > Img< UnsignedShortType > getElevationMap
( RandomAccessibleInterval< T > stack, RandomAccessibleInterval< UnsignedShortType > zMap, String method, int delta )
{
ImgFactory< UnsignedShortType > imgFactory = new ArrayImgFactory<>( new UnsignedShortType() );
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/Threshold.java b/src/main/java/fr/pasteur/ida/zellige/utils/Threshold.java
index 81afcb9a2eed4c52b89aa0808503bdf528d2e2c4..a4dc029d92aebf9ef39746c0aac196a559e8b45e 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/Threshold.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/Threshold.java
@@ -116,7 +116,7 @@ public class Threshold
// ported to ImageJ plugin by G.Landini
int ih;
- int threshold = - 1;
+ int threshold;
int num_pixels = 0;
double total_mean; /* mean gray-level for the whole image */
double bcv, term; /* between-class variance, scaling term */
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/VarianceFilter2D.java b/src/main/java/fr/pasteur/ida/zellige/utils/VarianceFilter2D.java
deleted file mode 100644
index bd53a0bbb00662f265f8e375ce3008b550f5be2d..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/utils/VarianceFilter2D.java
+++ /dev/null
@@ -1,100 +0,0 @@
-package fr.pasteur.ida.zellige.utils;
-
-import net.imglib2.Cursor;
-import net.imglib2.IterableInterval;
-import net.imglib2.RandomAccess;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.algorithm.neighborhood.Neighborhood;
-import net.imglib2.algorithm.neighborhood.RectangleShape;
-import net.imglib2.img.Img;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.RealType;
-import net.imglib2.view.IntervalView;
-import net.imglib2.view.Views;
-
-public class VarianceFilter2D<T extends RealType<T> & NativeType<T>> {
-
- private final Img<T> source;
-
- private final Img<T> output;
-
- private final int radius;
-
- /**
- * Instantiate a new variance filter that will operate on the specified
- * source.
- *
- * @param source the source to operate on.
- * @param radius determines the size of the neighborhood. In 2D or 3D, a radius
- * of 1 will generate a 3x3 neighborhood.
- */
- public VarianceFilter2D(final Img<T> source, final int radius) {
- this.source = source;
- this.radius = radius;
- this.output = source.factory().create(source.dimension( 0 ), source.dimension( 1 ), source.dimension( 2 ));
- }
-
- public void process() {
- final long nz = source.dimension(2);
- for (long z = 0; z < nz; z++) {
- final IntervalView<T> slice = Views.hyperSlice(source, 2, z);
- final IntervalView<T> outputSlice = Views.hyperSlice(output, 2, z);
- processSlice(slice, outputSlice);
- }
- }
-
- private void processSlice(final RandomAccessibleInterval<T> in, final IterableInterval<T> out) {
- final Cursor<T> cursor = out.cursor();
- final RectangleShape shape = new RectangleShape(radius, false);
- final RectangleShape.NeighborhoodsAccessible<T> accessible = shape.neighborhoodsRandomAccessible(Views.extendZero(in));
- final RandomAccess<Neighborhood<T>> nra = accessible.randomAccess(in);
-
- final int size = (int) nra.get().size();
- final double[] values = new double[size];
-
- while (cursor.hasNext()) {
- cursor.fwd();
- nra.setPosition(cursor);
- double v = computeVariance(nra, values);
- cursor.get().setReal( Math.sqrt( v ) ); /* Not variance but SD*/
- }
- }
-
-
- public static < T extends RealType< T > & NativeType< T > > double
- computeVariance(RandomAccess<Neighborhood<T>> nra, double[] values)
- {
- int index = 0;
- double sum = 0;
- for (final T pixel : nra.get())
- {
- double value = pixel.getRealDouble();
- values[index] = value;
- sum = sum + value;
- index++;
- }
- double mean = sum / ( index );
- return computeVariance( values, mean );
- }
-
-
-
-
-
- public static double computeVariance(double[] values, double mean) {
- double variance = 0;
- for (int i = 0; i <= values.length - 1; i++) {
- double v = values[i] - mean;
- double vSquare = v * v;
- variance = variance + (vSquare);
- }
- return variance / values.length;
-
- }
-
- public Img<T> getResult() {
- return output.copy();
- }
-
-
-}