From bfbd78bbe25e28b15621e6f67311de9c25f11afa Mon Sep 17 00:00:00 2001
From: Lorenzo ZOLFANELLI <lorenzo.zolfanelli@espci.psl.eu>
Date: Mon, 21 Mar 2022 14:52:34 +0100
Subject: [PATCH] added x coordiantes and rotation matrix readout

---
 nd2reader/parser.py       |  1 -
 nd2reader/raw_metadata.py | 62 ++++++++++++++++++++++++++++++++++++++-
 2 files changed, 61 insertions(+), 2 deletions(-)

diff --git a/nd2reader/parser.py b/nd2reader/parser.py
index 2f7b58d..bebbcaa 100644
--- a/nd2reader/parser.py
+++ b/nd2reader/parser.py
@@ -6,7 +6,6 @@ import six
 import warnings
 from pims.base_frames import Frame
 import numpy as np
-from tqdm import tqdm
 
 from nd2reader.common import get_version, read_chunk
 from nd2reader.label_map import LabelMap
diff --git a/nd2reader/raw_metadata.py b/nd2reader/raw_metadata.py
index 1152219..3c25d57 100644
--- a/nd2reader/raw_metadata.py
+++ b/nd2reader/raw_metadata.py
@@ -45,9 +45,13 @@ class RawMetadata(object):
             "frames": self._parse_frames(),
             "z_levels": self._parse_z_levels(),
             "z_coordinates": parse_if_not_none(self.z_data, self._parse_z_coordinates),
+            "x_coordinates": parse_if_not_none(self.x_data, self._parse_x_coordinates),
+            "y_coordinates": parse_if_not_none(self.y_data, self._parse_y_coordinates),
             "total_images_per_channel": frames_per_channel,
             "channels": self._parse_channels(),
-            "pixel_microns": parse_if_not_none(self.image_calibration, self._parse_calibration)
+            "pixel_microns": parse_if_not_none(self.image_calibration, self._parse_calibration),
+            "camera_stage_angle": parse_if_not_none(self.image_metadata_sequence, self._parse_camera_angle),
+            "camera_stage_matrix": parse_if_not_none(self.image_metadata_sequence, self._parse_camera_matrix)
         }
 
         self._set_default_if_not_empty('fields_of_view')
@@ -195,6 +199,62 @@ class RawMetadata(object):
         """
         return self.z_data.tolist()
 
+    def _parse_x_coordinates(self):
+        """The coordinate in micron for all x frames.
+
+        Returns:
+            list: the x coordinates in micron
+        """
+        return self.x_data.tolist()
+
+    def _parse_y_coordinates(self):
+        """The coordinate in micron for all y frames.
+
+        Returns:
+            list: the y coordinates in micron
+        """
+        return self.y_data.tolist()
+
+    def _parse_camera_angle(self):
+        if self.image_metadata_sequence is None:
+            return []
+
+        try:
+            metadata = self.image_metadata_sequence[six.b('SLxPictureMetadata')]
+        except KeyError:
+            return []
+
+        try:
+            return metadata[b'dAngle']
+        except KeyError:
+            return None
+
+    def _parse_camera_matrix(self):
+        if self.image_metadata_sequence is None:
+            return []
+
+        try:
+            metadata = self.image_metadata_sequence[six.b('SLxPictureMetadata')][b'sPicturePlanes']
+        except KeyError:
+            return []
+
+        validity = self._get_channel_validity_list(metadata)
+
+        channels = []
+        for valid, (label, chan) in zip(validity, sorted(metadata[b'sSampleSetting'].items())):
+            if not valid:
+                continue
+            if chan[b'matCameraToStage'] is not None:
+                mat_data = chan[b'matCameraToStage'][b'Data']
+                mat_rows = chan[b'matCameraToStage'][b'Rows']
+                mat_columns = chan[b'matCameraToStage'][b'Columns']
+                mat = np.frombuffer(mat_data, dtype=np.float64).reshape([mat_rows, mat_columns])
+                channels.append(mat)
+            else:
+                channels.append(None)
+        return channels
+
+
     def _parse_dimension_text(self):
         """While there are metadata values that represent a lot of what we want to capture, they seem to be unreliable.
         Sometimes certain elements don't exist, or change their data type randomly. However, the human-readable text