Merge pull request #151 from jimrybarski/150-remove-camera-settings

resolves #150, #149: removed camera settings entirely because they ar…

README.md

@@ -119,37 +119,6 @@ The `Nd2` object has some programmatically-accessible metadata:
 0.22
 ```
 
-Each camera has its own settings. If you image multiple wavelengths with one camera, each channel will appear as its
-own camera:
-
-```python
->>> nd2.camera_settings
-{'GFP': <Camera Settings: GFP>
-Camera: Andor Zyla VSC-00461
-Camera ID: VSC-00461
-Exposure Time (ms): 100.0
-Binning: 2x2, 'BF': <Camera Settings: BF>
-Camera: Andor Zyla VSC-00461
-Camera ID: VSC-00461
-Exposure Time (ms): 100.0
-Binning: 2x2}
-```
-
-Camera information can be accessed programmatically:
-
-```python
->>> nd2.camera_settings['GFP'].id
-'VSC-00461'
->>> nd2.camera_settings['GFP'].name
-'Andor Zyla VSC-00461'
->>> nd2.camera_settings['GFP'].exposure
-100.0
->>> nd2.camera_settings['GFP'].x_binning
-2
->>> nd2.camera_settings['GFP'].y_binning
-2
-```
-
 ### Contributing
 
 If you'd like to help with the development of nd2reader or just have an idea for improvement, please see the [contributing](https://github.com/jimrybarski/nd2reader/blob/master/CONTRIBUTING.md) page

ftest.py

@@ -1,7 +1,7 @@
 import unittest
 from functional_tests.FYLM141111001 import FYLM141111Tests
 from functional_tests.single import SingleTests
-from functional_tests.monocycle import Monocycle1Tests, Monocycle2Tests
+from functional_tests.monocycle import Monocycle1Tests, Monocycle2Tests, OneTests
 
 if __name__ == '__main__':
     unittest.main()

functional_tests/monocycle.py

@@ -136,3 +136,11 @@ class Monocycle2Tests(unittest.TestCase):
             n = image.index
             if n > 100:
                 break
+
+
+class OneTests(unittest.TestCase):
+    def test_opens(self):
+        # just testing that this doesn't throw an exception
+        nd2 = Nd2("/var/nd2s/001.nd2")
+        self.assertIsNotNone(nd2)
+        nd2.close()

nd2reader/__init__.py

@@ -1,3 +1,3 @@
 from nd2reader.main import Nd2
 
-__version__ = '2.1.1'
+__version__ = '2.1.2'

nd2reader/main.py

@@ -154,16 +154,6 @@ class Nd2(object):
         """
         return self._metadata.frames
 
-    @property
-    def camera_settings(self):
-        """
-        Basic information about the physical cameras used.
-
-        :return:    dict of {channel_name: model.metadata.CameraSettings}
-
-        """
-        return self._parser.camera_metadata
-    
     @property
     def date(self):
         """

nd2reader/parser/v3.py

@@ -141,7 +141,6 @@ class V3Parser(BaseParser):
             super(V3Parser, self).__init__(fh)
         self._label_map = self._build_label_map()
         self.raw_metadata = V3RawMetadata(self._fh, self._label_map)
-        self._parse_camera_metadata()
         self._parse_metadata()
 
     @property
@@ -152,15 +151,6 @@ class V3Parser(BaseParser):
         """
         return V3Driver(self.metadata, self._label_map, self._fh)
 
-    def _parse_camera_metadata(self):
-        """
-        Gets parsed data about the physical cameras used to produce images and throws them in a dictionary.
-
-        """
-        self.camera_metadata = {}
-        for camera_setting in self._parse_camera_settings():
-            self.camera_metadata[camera_setting.channel_name] = camera_setting
-            
     def _parse_metadata(self):
         """
         Reads all metadata and instantiates the Metadata object.
@@ -177,30 +167,6 @@ class V3Parser(BaseParser):
         pixel_microns = self.raw_metadata.image_calibration.get(six.b('SLxCalibration'), {}).get(six.b('dCalibration'))
         self.metadata = Metadata(height, width, channels, date, fields_of_view, frames, z_levels, total_images_per_channel, pixel_microns)
 
-    def _parse_camera_settings(self):
-        """
-        Looks up information in the raw metadata about the camera(s) and puts it into a CameraSettings object.
-        Duplicate cameras can be returned if the same one was used for multiple channels.
-
-        """
-        for n, camera in enumerate(self.raw_metadata.image_metadata_sequence[six.b('SLxPictureMetadata')][six.b('sPicturePlanes')][six.b('sSampleSetting')].values()):
-            name = camera[six.b('pCameraSetting')][six.b('CameraUserName')]
-            id = camera[six.b('pCameraSetting')][six.b('CameraUniqueName')]
-            exposure = camera[six.b('dExposureTime')]
-            x_binning = camera[six.b('pCameraSetting')][six.b('FormatFast')][six.b('fmtDesc')][six.b('dBinningX')]
-            y_binning = camera[six.b('pCameraSetting')][six.b('FormatFast')][six.b('fmtDesc')][six.b('dBinningY')]
-            optical_configs = camera[six.b('sOpticalConfigs')]
-
-            # This definitely is not working right. It seems to be totally inconsistent in each of the sample ND2s that I have.
-            # Fixing one breaks another.
-            if six.b('') in optical_configs.keys():
-                channel_name = optical_configs[six.b('')][six.b('sOpticalConfigName')]
-                yield CameraSettings(name, id, exposure, x_binning, y_binning, channel_name)
-            else:
-                channel_names = [channel[six.b('Name')] for key, channel in camera[six.b('pCameraSetting')][six.b('Metadata')][six.b('Channels')].items()]
-                for channel_name in channel_names:
-                    yield CameraSettings(name, id, exposure, x_binning, y_binning, channel_name)
-
     def _parse_date(self, raw_metadata):
         """
         The date and time when acquisition began.

setup.py

@@ -1,6 +1,6 @@
 from setuptools import setup
 
-VERSION = '2.1.1'
+VERSION = '2.1.2'
 
 if __name__ == '__main__':
     setup(