Added parsing for basic ROI metadata.

nd2reader/main.py

@@ -14,6 +14,7 @@ class Nd2(object):
         major_version, minor_version = get_version(self._fh)
         self._parser = get_parser(self._fh, major_version, minor_version)
         self._metadata = self._parser.metadata
+        self._roi_metadata = self._parser.roi_metadata
         
     def __repr__(self):
         return "\n".join(["<ND2 %s>" % self._filename,

nd2reader/model/roi.py

@@ -0,0 +1,63 @@
+import six
+import numpy as np
+
+
+class Roi(object):
+    """
+    A ND2 ROI representation.
+    Coordinates are the center coordinates of the ROI in (x, y, z) order.
+    Sizes are the sizes of the ROI in (x, y, z) order.
+    Shapes are represented by numbers, defined by constants in this class.
+    All these properties can be set for multiple timepoints.
+    """
+    SHAPE_RECTANGLE = 3
+    SHAPE_CIRCLE = 9
+
+    def __init__(self, raw_roi_dict):
+        self.timepoints = []
+        self.positions = []
+        self.sizes = []
+        self.shapes = []
+
+        self._extract_vect_anims(raw_roi_dict)
+
+    def _extract_vect_anims(self, raw_roi_dict):
+        """
+        Extract the vector animation parameters from the ROI.
+        This includes the position and size at the given timepoints.
+        :param raw_roi_dict:
+        :return:
+        """
+        number_of_timepoints = raw_roi_dict[six.b('m_vectAnimParams_Size')]
+
+        for i in range(number_of_timepoints):
+            shape = raw_roi_dict[six.b('m_sInfo')][six.b('m_uiShapeType')]
+            self._parse_vect_anim(raw_roi_dict[six.b('m_vectAnimParams_%d') % i], shape)
+
+        # convert to NumPy arrays
+        self.timepoints = np.array(self.timepoints, dtype=np.float)
+        self.positions = np.array(self.positions, dtype=np.float)
+        self.sizes = np.array(self.sizes, dtype=np.float)
+        self.shapes = np.array(self.shapes, dtype=np.uint)
+
+    def _parse_vect_anim(self, animation_dict, shape):
+        """
+        Parses a ROI vector animation object and adds it to the global list of timepoints and positions.
+        :param animation_dict:
+        :return:
+        """
+        self.timepoints.append(animation_dict[six.b('m_dTimeMs')])
+        self.positions.append((animation_dict[six.b('m_dCenterX')],
+                               animation_dict[six.b('m_dCenterY')],
+                               animation_dict[six.b('m_dCenterZ')]))
+        size_dict = animation_dict[six.b('m_sBoxShape')]
+        self.sizes.append((size_dict[six.b('m_dSizeX')],
+                           size_dict[six.b('m_dSizeY')],
+                           size_dict[six.b('m_dSizeZ')]))
+        self.shapes.append(shape)
+
+    def is_circle(self, timepoint_id=0):
+        return self.shapes[timepoint_id] == self.SHAPE_CIRCLE
+
+    def is_rectangle(self, timepoint_id=0):
+        return self.shapes[timepoint_id] == self.SHAPE_RECTANGLE

nd2reader/parser/base.py

@@ -6,6 +6,7 @@ class BaseParser(object):
         self._fh = fh
         self.camera_metadata = None
         self.metadata = None
+        self.roi_metadata = None
 
     @abstractproperty
     def driver(self):

nd2reader/parser/v3.py

@@ -3,6 +3,7 @@
 from datetime import datetime
 from nd2reader.model.metadata import Metadata
 from nd2reader.model.label import LabelMap
+from nd2reader.model.roi import Roi
 from nd2reader.parser.base import BaseParser
 from nd2reader.driver.v3 import V3Driver
 from nd2reader.common.v3 import read_chunk, read_array, read_metadata
@@ -18,6 +19,7 @@ def ignore_missing(func):
             return func(*args, **kwargs)
         except:
             return None
+
     return wrapper
 
 
@@ -142,6 +144,7 @@ class V3Parser(BaseParser):
         self._label_map = self._build_label_map()
         self.raw_metadata = V3RawMetadata(self._fh, self._label_map)
         self._parse_metadata()
+        self._parse_roi_metadata()
 
     @property
     def driver(self):
@@ -165,7 +168,8 @@ class V3Parser(BaseParser):
         total_images_per_channel = self._parse_total_images_per_channel(self.raw_metadata)
         channels = self._parse_channels(self.raw_metadata)
         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)
+        self.metadata = Metadata(height, width, channels, date, fields_of_view, frames, z_levels,
+                                 total_images_per_channel, pixel_microns)
 
     def _parse_date(self, raw_metadata):
         """
@@ -205,7 +209,8 @@ class V3Parser(BaseParser):
         channels = []
         metadata = raw_metadata.image_metadata_sequence[six.b('SLxPictureMetadata')][six.b('sPicturePlanes')]
         try:
-            validity = raw_metadata.image_metadata[six.b('SLxExperiment')][six.b('ppNextLevelEx')][six.b('')][0][six.b('ppNextLevelEx')][six.b('')][0][six.b('pItemValid')]
+            validity = raw_metadata.image_metadata[six.b('SLxExperiment')][six.b('ppNextLevelEx')][six.b('')][0][
+                six.b('ppNextLevelEx')][six.b('')][0][six.b('pItemValid')]
         except (KeyError, TypeError):
             # If none of the channels have been deleted, there is no validity list, so we just make one
             validity = [True for _ in metadata]
@@ -303,6 +308,26 @@ class V3Parser(BaseParser):
         """
         return raw_metadata.image_attributes[six.b('SLxImageAttributes')][six.b('uiSequenceCount')]
 
+    def _parse_roi_metadata(self):
+        """
+        Parse the raw ROI metadata.
+        :return:
+        """
+        if not six.b('RoiMetadata_v1') in self.raw_metadata.roi_metadata:
+            self.roi_metadata = None
+            return
+
+        raw_roi_data = self.raw_metadata.roi_metadata[six.b('RoiMetadata_v1')]
+
+        number_of_rois = raw_roi_data[six.b('m_vectGlobal_Size')]
+
+        roi_objects = []
+        for i in range(number_of_rois):
+            current_roi = raw_roi_data[six.b('m_vectGlobal_%d' % i)]
+            roi_objects.append(Roi(current_roi))
+
+        self.roi_metadata = roi_objects
+
     def _build_label_map(self):
         """
         Every label ends with an exclamation point, however, we can't directly search for those to find all the labels