diff --git a/docs b/docs
index 438ef091834dbeab162f0255ff81db3396623b2a..f3f986bb87ac932bc45fc494c7b72fa485848a87 160000
--- a/docs
+++ b/docs
@@ -1 +1 @@
-Subproject commit 438ef091834dbeab162f0255ff81db3396623b2a
+Subproject commit f3f986bb87ac932bc45fc494c7b72fa485848a87
diff --git a/nd2reader/__init__.py b/nd2reader/__init__.py
index eb2f484616bb29a6d76eeca43e57579b71f360c5..8ecf55219a569186117b66d2c07513b6a3e51b38 100644
--- a/nd2reader/__init__.py
+++ b/nd2reader/__init__.py
@@ -1,4 +1,4 @@
from nd2reader.reader import ND2Reader
from nd2reader.legacy import Nd2
-__version__ = '3.0.5'
+__version__ = '3.0.6'
diff --git a/nd2reader/reader.py b/nd2reader/reader.py
index b27259c1d186cebf769a89e12858c94fe3ac453d..30c3c1e8baf22e45dc6cfa11790b4b319b033471 100644
--- a/nd2reader/reader.py
+++ b/nd2reader/reader.py
@@ -1,4 +1,4 @@
-from pims.base_frames import FramesSequenceND, Frame
+from pims.base_frames import FramesSequenceND
from nd2reader.exceptions import EmptyFileError
from nd2reader.parser import Parser
@@ -52,7 +52,7 @@ class ND2Reader(FramesSequenceND):
except KeyError:
return 0
- def get_frame_2D(self, c=0, t=0, z=0, x=0, y=0):
+ def get_frame_2D(self, c=0, t=0, z=0, x=0, y=0, v=0):
"""Gets a given frame using the parser
Args:
@@ -61,6 +61,7 @@ class ND2Reader(FramesSequenceND):
c: The color channel number
t: The frame number
z: The z stack number
+ v: The field of view index
Returns:
numpy.ndarray: The requested frame
@@ -73,7 +74,7 @@ class ND2Reader(FramesSequenceND):
x = self.metadata["width"] if x <= 0 else x
y = self.metadata["height"] if y <= 0 else y
- return self._parser.get_image_by_attributes(t, 0, c_name, z, y, x)
+ return self._parser.get_image_by_attributes(t, v, c_name, z, y, x)
@property
def parser(self):
@@ -136,6 +137,7 @@ class ND2Reader(FramesSequenceND):
self._init_axis_if_exists('c', len(self._get_metadata_property("channels", default=[])), min_size=2)
self._init_axis_if_exists('t', len(self._get_metadata_property("frames", default=[])))
self._init_axis_if_exists('z', len(self._get_metadata_property("z_levels", default=[])), min_size=2)
+ self._init_axis_if_exists('v', len(self._get_metadata_property("fields_of_view", default=[])), min_size=2)
if len(self.sizes) == 0:
raise EmptyFileError("No axes were found for this .nd2 file.")
@@ -153,7 +155,7 @@ class ND2Reader(FramesSequenceND):
Returns:
the axis to iterate over
"""
- priority = ['t', 'z', 'c']
+ priority = ['t', 'z', 'c', 'v']
found_axes = []
for axis in priority:
try:
diff --git a/setup.py b/setup.py
index 5d48b11eea1bea61d6cb14b18ac69aa62dc662e4..77a3fa2701a8d5c4a059158870d389ddcc5e21e9 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,6 @@
from setuptools import setup
-VERSION = '3.0.5'
+VERSION = '3.0.6'
if __name__ == '__main__':
setup(
diff --git a/sphinx/conf.py b/sphinx/conf.py
index 1c618a2ede656382eb5285832f924308c564e151..fc42bf521c7bb9cfc8089355c2c8585d4b5540e0 100644
--- a/sphinx/conf.py
+++ b/sphinx/conf.py
@@ -44,9 +44,9 @@ author = 'Ruben Verweij'
# built documents.
#
# The short X.Y version.
-version = '3.0.5'
+version = '3.0.6'
# The full version, including alpha/beta/rc tags.
-release = '3.0.5'
+release = '3.0.6'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
diff --git a/sphinx/tutorial.md b/sphinx/tutorial.md
index 932fc04af0d166a823a66db79b5829cda5924b7a..6be8c494ee3fad9ec2b5c7119ce47797b86d97a7 100644
--- a/sphinx/tutorial.md
+++ b/sphinx/tutorial.md
@@ -57,7 +57,6 @@ from nd2reader import ND2Reader
with ND2Reader('my_directory/example.nd2') as images:
# width and height of the image
print('%d x %d px' % (images.metadata['width'], images.metadata['height']))
-
```
All metadata properties are:
@@ -74,4 +73,47 @@ All metadata properties are:
* `rois`: the regions of interest (ROIs) defined by the user
* `experiment`: information about the nature and timings of the ND experiment
+### Iterating over fields of view
+
+Using `NDExperiments` in the Nikon software, it is possible to acquire images on different `(x, y)` positions.
+This is referred to as different fields of view. Using this reader, the fields of view are on the `v` axis.
+For example:
+```python
+from nd2reader import ND2Reader
+with ND2Reader('my_directory/example.nd2') as images:
+ # width and height of the image
+ print(images.metadata)
+```
+will output
+```python
+{'channels': ['BF100xoil-1x-R', 'BF+RITC'],
+ 'date': datetime.datetime(2017, 10, 30, 14, 35, 18),
+ 'experiment': {'description': 'ND Acquisition',
+ 'loops': [{'duration': 0,
+ 'sampling_interval': 0.0,
+ 'start': 0,
+ 'stimulation': False}]},
+ 'fields_of_view': [0, 1],
+ 'frames': [0],
+ 'height': 1895,
+ 'num_frames': 1,
+ 'pixel_microns': 0.09214285714285715,
+ 'total_images_per_channel': 6,
+ 'width': 2368,
+ 'z_levels': [0, 1, 2]}
+```
+for our example file. As you can see from the metadata, it has two fields of view. We can also look at the sizes of the axes:
+```python
+ print(images.sizes)
+```
+```python
+{'c': 2, 't': 1, 'v': 2, 'x': 2368, 'y': 1895, 'z': 3}
+```
+As you can see, the fields of view are listed on the `v` axis. It is therefore possible to loop over them like this:
+```python
+ images.iter_axes = 'v'
+ for fov in images:
+ print(fov) # Frame containing one field of view
+```
+For more information on axis bundling and iteration, refer to the [pims documentation](http://soft-matter.github.io/pims/v0.4/multidimensional.html#axes-bundling).