diff --git a/COPYING b/COPYING
index 7cd7b82385b43a76797fb2995e55da74a5b153eb..b242b98048e8f58273f4b4458f534129eededd92 100644
--- a/COPYING
+++ b/COPYING
@@ -1,4 +1,5 @@
Copyright 2014-2016 Jim Rybarski, 2017 Ruben Verweij
+Copyright 2020-2021 Lorenzo Zolfanelli, ESPCI Paris - PSL
nd2reader is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
diff --git a/nd2reader/parser.py b/nd2reader/parser.py
index 8534e7996fad76eec9c1e85efe55caefb0d3d4bf..bebbcaa0a731d243b253f9566177f50c0140b57e 100644
--- a/nd2reader/parser.py
+++ b/nd2reader/parser.py
@@ -78,6 +78,38 @@ class Parser(object):
else:
return Frame(image, frame_no=frame_number, metadata=self._get_frame_metadata())
+ def get_slice_by_attributes(self, xywh, frame_number, field_of_view, channel, z_level, height, width):
+ """Gets a rectangular slice of an image based on its attributes alone
+
+ Args:
+ xywh: tuples containing (x, y, w, h) values of the
+ rectangular region to load
+ frame_number: the frame number
+ field_of_view: the field of view
+ channel_name: the color channel name
+ z_level: the z level
+ height: the height of the image
+ width: the width of the image
+
+ Returns:
+ Frame: the requested image
+
+ """
+ frame_number = 0 if frame_number is None else frame_number
+ field_of_view = 0 if field_of_view is None else field_of_view
+ channel = 0 if channel is None else channel
+ z_level = 0 if z_level is None else z_level
+
+ image_group_number = self._calculate_image_group_number(frame_number, field_of_view, z_level)
+ try:
+ timestamp, raw_image_data = self._get_raw_slice_data(
+ xywh, image_group_number, channel, height, width
+ )
+ except (TypeError):
+ return Frame([], frame_no=frame_number, metadata=self._get_frame_metadata())
+ else:
+ return Frame(raw_image_data, frame_no=frame_number, metadata=self._get_frame_metadata())
+
def get_image_by_attributes(self, frame_number, field_of_view, channel, z_level, height, width):
"""Gets an image based on its attributes alone
@@ -246,6 +278,79 @@ class Parser(object):
"""
return {channel: n for n, channel in enumerate(self.metadata["channels"])}
+ def _get_raw_slice_data(self, xywh, image_group_number, channel, height, width):
+ """Reads the raw bytes and the timestamp of a rectangular slice
+ of an image.
+
+ Args:
+ xywh: tuples containing (x, y, w, h) values of the
+ rectangular region to load
+ image_group_number: the image group number (see _calculate_image_group_number)
+ channel: the position (int) of the channel to load
+ height: the height of the image
+ width: the width of the image
+
+ Returns:
+
+ """
+ size_c = len(self.metadata["channels"])
+
+ x0, y0, w, h = xywh
+ chunk_location = self._label_map.get_image_data_location(image_group_number)
+ fh = self._fh
+
+ if chunk_location is None or fh is None:
+ return None
+ fh.seek(chunk_location)
+ # The chunk metadata is always 16 bytes long
+ chunk_metadata = fh.read(16)
+ header, relative_offset, data_length = struct.unpack("IIQ", chunk_metadata)
+ if header != 0xabeceda:
+ raise ValueError("The ND2 file seems to be corrupted.")
+ # We start at the location of the chunk metadata, skip over the metadata, and then proceed to the
+ # start of the actual data field, which is at some arbitrary place after the metadata.
+ fh.seek(chunk_location + 16 + relative_offset)
+
+ # Read timestamp (8 bytes)
+ timestamp = struct.unpack("d", fh.read(8))[0]
+
+ # Stitched Images: evaluate number of bytes to strip
+ # (with stitched images sometimes after each row we have a regular number of extra bytes)
+ n_unwanted_bytes = (data_length-8) % (height*width)
+ assert 0 == n_unwanted_bytes % height
+ rowskip = n_unwanted_bytes // height
+
+ # Read ROI: row-by-row
+ image_start_pos = chunk_location + 16 + relative_offset + 8
+
+ line_bytemask = np.zeros(size_c, dtype=np.bool)
+ line_bytemask[channel] = True
+ line_bytemask = np.tile(line_bytemask.repeat(2),w)
+
+ def get_line(y):
+ fh.seek(image_start_pos + size_c*2*((width)*y+x0) + y*rowskip)
+ return np.frombuffer(fh.read(size_c*2*w), np.byte)[line_bytemask]
+
+ data = [get_line(y) for y in range(y0, y0+h)]
+ data = bytes().join(data)
+
+ image_group_data = array.array("H", data)
+ true_channels_no = int(len(image_group_data) / (h * w))
+
+ image_data = np.reshape(image_group_data, (h, w, true_channels_no))
+
+ missing_channels = ~np.any(image_data, axis=(0, 1))
+ image_data[..., missing_channels] = np.full(
+ (h, w, missing_channels.sum()), np.nan)
+
+ if np.any(missing_channels):
+ warnings.warn(
+ "ND2 file contains gap frames which are represented by "
+ + "np.nan-filled arrays; to convert to zeros use e.g. "
+ + "np.nan_to_num(array)")
+ return timestamp, image_data[...,0]
+
+
def _get_raw_image_data(self, image_group_number, channel_offset, height, width):
"""Reads the raw bytes and the timestamp of an image.
diff --git a/nd2reader/raw_metadata.py b/nd2reader/raw_metadata.py
index 11522196f4026a56605956251bab60d12994f423..3c25d576cfcd9d9c393e3ab2886c9a86ccf918e2 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
diff --git a/nd2reader/reader.py b/nd2reader/reader.py
index 4e14f42e3cd37f39f59ffb9dd5624c1a32287c82..295bded08427ac578f4bd0197fac6c52bd892464 100644
--- a/nd2reader/reader.py
+++ b/nd2reader/reader.py
@@ -69,6 +69,21 @@ class ND2Reader(FramesSequenceND):
except KeyError:
return 0
+ def get_roi(self, roi, c=0, t=0, z=0, x=0, y=0, v=0):
+ height = self.metadata['height']
+ width = self.metadata['width']
+ ylim = roi[0].indices(height)
+ xlim = roi[1].indices(width)
+
+ y = ylim[0]
+ x = xlim[0]
+ w = xlim[1]-xlim[0]
+ h = ylim[1]-ylim[0]
+
+ return self._parser.get_slice_by_attributes(
+ (x, y, w, h), t, v, c, z, height, width
+ )
+
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:
diff --git a/setup.py b/setup.py
index c5dde1c857064f2449080fe28ca756d603fda5f6..5b6ebdd4cca15cf3810e29f26b6ffda85e834c59 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,5 @@
from setuptools import setup
-
-VERSION = '3.3.0'
+#from nd2reader import __version__ as VERSION
if __name__ == '__main__':
setup(
@@ -10,15 +9,15 @@ if __name__ == '__main__':
'numpy>=1.14',
'six>=1.4',
'xmltodict>=0.9.2',
- 'pims>=0.3.0'
+ 'PIMS>=0.5.0'
],
python_requires=">=3.6",
- version=VERSION,
+ version="3.2.3-zolfa-dev0",
description='A tool for reading ND2 files produced by NIS Elements',
author='Ruben Verweij',
author_email='ruben@lighthacking.nl',
url='https://github.com/rbnvrw/nd2reader',
- download_url='https://github.com/rbnvrw/nd2reader/tarball/%s' % VERSION,
+ download_url='https://github.com/rbnvrw/nd2reader/tarball/%s' % "3.2.3-zolfa-dev0",
keywords=['nd2', 'nikon', 'microscopy', 'NIS Elements'],
classifiers=['Development Status :: 5 - Production/Stable',
'Intended Audience :: Science/Research',