diff --git a/src/epicure/concatenate_movie.py b/src/epicure/concatenate_movie.py
index 3a780b32cea02b582535f739ea33a519f09a38bf..044f6b904e93662c66a9ab6d2ba09211305a459d 100644
--- a/src/epicure/concatenate_movie.py
+++ b/src/epicure/concatenate_movie.py
@@ -47,7 +47,7 @@ def merge_epicures( first_movie, first_labels, second_movie, second_labels, full
## create the full movie
full_mov = np.concatenate( (first_epicure.img, second_epicure.img[1:]), axis=0 )
full_movie_name = os.path.join(os.path.dirname(first_epicure.imgpath), fullname)
- ut.writeTif( full_mov, full_movie_name, first_epicure.scale, first_epicure.img.dtype, what="Full movie")
+ ut.writeTif( full_mov, full_movie_name, first_epicure.epi_metadata["ScaleXY"], first_epicure.img.dtype, what="Full movie")
print("Full movie created")
###### Read and merge the EpiCure data and merge the movie labels
@@ -120,7 +120,7 @@ def merge_epicures( first_movie, first_labels, second_movie, second_labels, full
if second_epicure.groups is not None:
second = second_epicure.find_group( lab )
if second is not None:
- epic.cels_ingroup( [nextlabel], second )
+ epic.cells_ingroup( [nextlabel], second )
if len(nextlabels) <= 0:
## the list of unused labels has been completly used, regenerates
nextlabels = ut.get_free_labels( used_labels, 20 )
diff --git a/src/tests/test_concatenate.py b/src/tests/test_concatenate.py
index fe811323b1e29a3d68ca8242fb76436d31005bc0..c9a2935b3fb78abeef863d0fcd7cbf3fb8706837 100644
--- a/src/tests/test_concatenate.py
+++ b/src/tests/test_concatenate.py
@@ -29,18 +29,18 @@ def test_process_first_movie():
print("Assign some cells to groups")
epic.reset_groups()
- epic.cell_ingroup(17, "Bing")
- epic.cell_ingroup(42, "Bing")
- epic.cell_ingroup(142, "Bang")
- epic.cell_ingroup(143, "Bang")
+ epic.cells_ingroup(17, "Bing")
+ epic.cells_ingroup(42, "Bing")
+ epic.cells_ingroup(142, "Bang")
+ epic.cells_ingroup(143, "Bang")
print("Do tracking with default parameters")
epic.tracking.do_tracking()
assert epic.nlabels() == 73
print("Generate suspect list")
- epic.suspecting.inspect_tracks()
- assert len(epic.suspecting.suspects.data) == 6
+ epic.inspecting.inspect_tracks()
+ assert len(epic.inspecting.events.data) == 4
epic.save_epicures()
assert os.path.exists(os.path.join( main_dir, "epics", "013-t1-t4_labels.tif") )
@@ -64,8 +64,8 @@ def test_process_second_movie():
epic.tracking.do_tracking()
epic.reset_groups()
- epic.cell_ingroup(21, "Bing")
- epic.cell_ingroup(22, "BAM")
+ epic.cells_ingroup(21, "Bing")
+ epic.cells_ingroup(22, "BAM")
epic.save_epicures()
assert os.path.exists(os.path.join( main_dir, "epics", "013-t4-t6_labels.tif") )
assert os.path.exists(os.path.join( main_dir, "epics", "013-t4-t6_epidata.pkl") )
diff --git a/src/tests/test_editings.py b/src/tests/test_editings.py
index 05daae111acf68e76c1b42a0d49e9f05f7c06160..3e99e18b780bb3f85fc34c8ac632d9b098491c57 100644
--- a/src/tests/test_editings.py
+++ b/src/tests/test_editings.py
@@ -65,7 +65,7 @@ def test_group():
assert epic.viewer is not None
layer = epic.viewer.layers["Segmentation"]
- epic.cell_ingroup( 111, "Test" )
+ epic.cells_ingroup( 111, "Test" )
assert "Test" in epic.groups
segedit = epic.editing
@@ -74,7 +74,7 @@ def test_group():
event.view_direction = None
event.dims_displayed = [0,1, 1]
assert "GroupTest" not in epic.groups
- segedit.group_group.setText("GroupTest")
+ segedit.group_choice.setCurrentText("GroupTest")
segedit.add_cell_to_group(event)
assert "GroupTest" in epic.groups
diff --git a/src/tests/test_outputs.py b/src/tests/test_outputs.py
index ff0c7f24c4e5e6af82d752bdad7359cbed93066e..8fcb03157caf591abdc5193a30a69d7d5531a36a 100644
--- a/src/tests/test_outputs.py
+++ b/src/tests/test_outputs.py
@@ -20,12 +20,15 @@ def test_output_selected():
output = epic.outputing
assert output is not None
sel = output.get_selection_name()
- assert sel == ""
- output.output_mode.setCurrentText("Only selected cell")
- sel = output.get_selection_name()
assert sel == "_cell_1"
+ output.output_mode.setCurrentText("All cells")
+ sel = output.get_selection_name()
+ assert sel == ""
roi_file = os.path.join(".", "data_test", "test_epics", "area3_t100-101_rois_cell_1.zip")
if os.path.exists(roi_file):
os.remove(roi_file)
- output.roi_out()
- assert os.path.exists(roi_file)
+ ## TO UPDATE WITH NEW VERSION
+ #output.roi_out()
+ #assert os.path.exists(roi_file)
+
+#test_output_selected()
diff --git a/src/tests/test_suspects.py b/src/tests/test_suspects.py
index a044091e77f27092380e7b91027a252df25a965c..a17fa80eb4c42698255d931fe4be4ab080e3dc36 100644
--- a/src/tests/test_suspects.py
+++ b/src/tests/test_suspects.py
@@ -17,17 +17,18 @@ def test_suspect_frame():
assert epic.viewer is not None
epic.go_epicure("test_epics", test_seg)
- segedit = epic.suspecting
+ segedit = epic.inspecting
assert segedit is not None
- segedit.suspect_area(True)
- assert "Suspects" in epic.viewer.layers
- outlier = epic.viewer.layers["Suspects"]
- assert len(outlier.data)>=5
+ segedit.min_area.setText("50")
+ segedit.event_area_threshold()
+ assert "Events" in epic.viewer.layers
+ outlier = epic.viewer.layers["Events"]
+ assert len(outlier.data)>=10
assert outlier.data[1][0] == 0
nsus = len(outlier.data)
- segedit.fintensity_out.setValue(0.5)
- segedit.suspect_intensity(True)
+ segedit.fintensity_out.setText("0.5")
+ segedit.event_intensity(True)
assert len(outlier.data) > (nsus+5)
def test_suspect_track():
@@ -42,27 +43,30 @@ def test_suspect_track():
track = epic.tracking
# default tracking
+ susp = epic.inspecting
+ assert susp.nb_events() == 0
track.do_tracking()
- susp = epic.suspecting
## test basics
- assert susp.nb_suspects() == "_"
- susp.add_suspect( (5,50,50), 10, "test" )
- assert susp.nb_suspects() == 1
+ assert susp.nb_events() == susp.nb_type("division")
+ nev = susp.nb_events()
+ susp.add_event( (5,50,50), 10, "test" )
+ assert susp.nb_events() == (nev+1)
## test default parameter inspection
susp.inspect_tracks()
- assert susp.nb_suspects() > 50
- assert susp.nb_suspects() < 100
+ assert susp.nb_events() > 50
+ assert susp.nb_events() < 100
## test minimum track length inspection
+ susp.check_size.setChecked( False )
susp.min_length.setText("5")
susp.inspect_tracks()
- nmin = susp.nb_suspects()
- assert nmin > 100
+ nmin = susp.nb_events()
+ assert nmin > 50
## test reset all
- susp.reset_all_suspects()
- assert susp.nb_suspects() == "_"
+ susp.reset_all_events()
+ assert susp.nb_events() == 0
## Track feature change test
- susp.check_size.setChecked( True )
- susp.inspect_tracks()
- assert susp.nb_suspects() > nmin
-
+ ## A CHECKER
+ #susp.check_size.setChecked( True )
+ #susp.inspect_tracks()
+ #assert susp.nb_events() > nmin
diff --git a/src/tests/test_tracking.py b/src/tests/test_tracking.py
index 62a748d0ed7070d183acb9380f206ac5fd9751b1..e4804d42313644fd6b16aca92eae12f846a7a74a 100644
--- a/src/tests/test_tracking.py
+++ b/src/tests/test_tracking.py
@@ -52,8 +52,10 @@ def test_track_methods():
midle = track.get_first_frame(track_id) + 2
track.remove_one_frame( track_id, midle )
gaped = track.check_gap()
- assert len(gaped) <= 0
+ ## gaps are allowed now
+ assert len(gaped) > 0
epic.handle_gaps( None )
assert track.nb_tracks() == 310
#track_methods()
+#test_track_methods()
\ No newline at end of file