From 3b53a74f6599202866f019d02524aaf82e66e143 Mon Sep 17 00:00:00 2001
From: jim <jim@rybarski.com>
Date: Tue, 11 Nov 2014 11:48:11 -0600
Subject: [PATCH] don't show cropped channels

---
 nd2reader/__init__.py | 26 ++++++++++++++++++++++----
 run.py                |  7 ++-----
 2 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/nd2reader/__init__.py b/nd2reader/__init__.py
index d59fcee..f70c1c5 100644
--- a/nd2reader/__init__.py
+++ b/nd2reader/__init__.py
@@ -28,9 +28,19 @@ class Nd2(object):
 
     @property
     def fields_of_view(self):
-        fov_data = self.metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx']['']
-        valid_fields = list(fov_data['pItemValid'])
-        for number, (fov, valid) in enumerate(zip(fov_data['uLoopPars']['Points'][''], valid_fields)):
+        """
+        Fields of view are the various places in the xy-plane where images were taken.
+
+        """
+        # Grab all the metadata about fields of view
+        fov_metadata = self.metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx']['']
+        # The attributes include x, y, and z coordinates, and perfect focus (PFS) offset
+        fov_attributes = fov_metadata['uLoopPars']['Points']['']
+        # If you crop fields of view from your ND2 file, the metadata is retained and only this list is
+        # updated to indicate that the fields of view have been deleted.
+        fov_validity = fov_metadata['pItemValid']
+        # We only yield valid (i.e. uncropped) fields of view
+        for number, (fov, valid) in enumerate(zip(fov_attributes, fov_validity)):
             if valid:
                 yield field_of_view(number=number + 1,
                                     x=fov['dPosX'],
@@ -52,10 +62,13 @@ class Nd2(object):
     @property
     def channels(self):
         metadata = self.metadata['ImageMetadataSeq']['SLxPictureMetadata']['sPicturePlanes']
+        validity = self.metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx']['']['ppNextLevelEx']['']['pItemValid']
         # Channel information is contained in dictionaries with the keys a0, a1...an where the number
         # indicates the order in which the channel is stored. So by sorting the dicts alphabetically
         # we get the correct order.
-        for label, chan in sorted(metadata['sPlaneNew'].items()):
+        for (label, chan), valid in zip(sorted(metadata['sPlaneNew'].items()), validity):
+            if not valid:
+                continue
             name = chan['sDescription']
             exposure_time = metadata['sSampleSetting'][label]['dExposureTime']
             camera = metadata['sSampleSetting'][label]['pCameraSetting']['CameraUserName']
@@ -65,6 +78,11 @@ class Nd2(object):
     def channel_count(self):
         return self.metadata['ImageAttributes']["SLxImageAttributes"]["uiComp"]
 
+    @property
+    def zoom_levels(self):
+        for i in self.metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx']['']['ppNextLevelEx'][''].items():
+            yield i
+
     @property
     def z_level_count(self):
         """
diff --git a/run.py b/run.py
index 3b8c2e4..6333009 100644
--- a/run.py
+++ b/run.py
@@ -11,11 +11,8 @@ n = Nd2("/home/jim/Desktop/nd2hacking/YFP-dsRed-GFP-BF.nd2")
 # for fov in n.fields_of_view:
 #     print(fov.number, fov.x, fov.y, fov.z, fov.pfs_offset)
 #
-print(n.timepoint_count)
-print(n.fov_count)
-print(n.channel_count)
-for fov in n.fields_of_view:
-    print(fov.number, fov.x, fov.y, fov.z)
+for chan in n.channels:
+    print(chan.name, chan.camera)
 # pprint(len(n.metadata['ImageMetadata']['SLxExperiment']['uLoopPars']['pPeriod']['']))
 
 # res = n.get_image(6)