Update stitched.py

Fixes rbnvrw/nd2reader#56.

.codeclimate.yml

@@ -1,15 +0,0 @@
-engines:
-  duplication:
-    enabled: true
-    config:
-      languages:
-        - python
-  fixme:
-    enabled: true
-  radon:
-    enabled: true
-ratings:
-  paths:
-    - "**.py"
-exclude_paths:
-  - tests/

.github/workflows/python-package.yml

@@ -0,0 +1,40 @@
+name: Build
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Install as package
+      run: |
+        python setup.py develop
+    - name: Test with pytest
+      run: |
+        pytest

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "docs"]
 	path = docs
-	url = https://github.com/rbnvrw/nd2reader.git
+	url = git@github.com:rbnvrw/nd2reader.git
 	branch = gh-pages

.travis.yml

@@ -1,33 +0,0 @@
-env:
-  global:
-    - CC_TEST_REPORTER_ID=8582900c285e4da0f253555b1bac1ba501bd6ff07850b0f227166b3cdac59ecc
-    
-language: python
-
-git:
-  depth: 3
-  
-notifications:
-  email: false
-
-python:
-  - 3.5
-  - 3.6
-  - 3.7
-  - 3.8
-
-install:
-  - pip install --upgrade pip setuptools wheel
-  - pip install --only-binary=numpy numpy
-  - pip install -r requirements.txt
-  - pip install 'coverage>=4.0,<4.4' --force-reinstall # Upstream bug: https://github.com/nedbat/coveragepy/issues/578
-  
-before_script:
-  - curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter
-  - chmod +x ./cc-test-reporter
-  - ./cc-test-reporter before-build
-  
-script: python ./test.py
-
-after_script:
-  - ./cc-test-reporter after-build --exit-code $TRAVIS_TEST_RESULT

MANIFEST.in

@@ -1,6 +1,6 @@
 include MANIFEST.in
-include VERSION
 include setup.py
+include setup.cfg
 include README.md
 include LICENSE
 include COPYING

README.md

@@ -2,9 +2,7 @@
 
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/nd2reader/badges/version.svg)](https://anaconda.org/conda-forge/nd2reader)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/nd2reader/badges/downloads.svg)](https://anaconda.org/conda-forge/nd2reader)
-[![Build Status](https://travis-ci.org/rbnvrw/nd2reader.svg?branch=master)](https://travis-ci.org/rbnvrw/nd2reader)
-[![Test Coverage](https://codeclimate.com/github/rbnvrw/nd2reader/badges/coverage.svg)](https://codeclimate.com/github/rbnvrw/nd2reader/coverage)
-[![Code Climate](https://codeclimate.com/github/rbnvrw/nd2reader/badges/gpa.svg)](https://codeclimate.com/github/rbnvrw/nd2reader)
+[![Build status](https://github.com/rbnvrw/nd2reader/actions/workflows/python-package.yml/badge.svg)](https://github.com/rbnvrw/nd2reader/actions/workflows/python-package.yml)
 
 ### About
 

docs

@@ -1 +1 @@
-Subproject commit f700c239f8f9d7d1f99a3c10d9f67e2b3b8ef307
+Subproject commit 42dbfdf18e0ed7656ef73ac66e889c3138ef756f

nd2reader/__init__.py

@@ -2,4 +2,12 @@ from os import path
 from nd2reader.reader import ND2Reader
 from nd2reader.legacy import Nd2
 
-__version__ = '3.2.3'
+try:
+    import importlib.metadata as importlib_metadata
+except:
+    import importlib_metadata
+
+try:
+    __version__ = importlib_metadata.version(__name__)
+except:
+    print('Unable to read version number')

nd2reader/stitched.py

@@ -1,40 +1,29 @@
 # -*- coding: utf-8 -*-
 import numpy as np  # type: ignore
-import warnings
 
 
 def get_unwanted_bytes_ids(image_group_data, image_data_start, height, width):
     # Check if the byte array size conforms to the image axes size. If not, check
     # that the number of unexpected (unwanted) bytes is a multiple of the number of
-    # rows (height), as the same unmber of unwanted bytes is expected to be
+    # rows (height), as the same number of unwanted bytes is expected to be
     # appended at the end of each row. Then, returns the indexes of the unwanted
     # bytes.
+    # Skip the first 4 elements that correspond to the time stamp
     number_of_true_channels = int(len(image_group_data[4:]) / (height * width))
-    n_unwanted_bytes = (len(image_group_data[image_data_start:])) % (height * width)
+    n_unwanted_bytes = (len(image_group_data[4:])) % (height * width)
     if not n_unwanted_bytes:
         return np.arange(0)
     assert 0 == n_unwanted_bytes % height, (
-        "An unexpected number of extra bytes was encountered based on the expected"
-        + " frame size, therefore the file could not be parsed."
+            "An unexpected number of extra bytes was encountered based on the expected"
+            + " frame size, therefore the file could not be parsed."
     )
     return np.arange(
-        image_data_start + height * number_of_true_channels,
+        image_data_start + width * number_of_true_channels,
         len(image_group_data) - n_unwanted_bytes + 1,
-        height * number_of_true_channels,
+        width * number_of_true_channels,
     )
 
 
-def remove_bytes_by_id(byte_ids, image_group_data, height):
-    # Remove bytes by ID.
-    bytes_per_row = len(byte_ids) // height
-    warnings.warn(
-        f"{len(byte_ids)} ({bytes_per_row}*{height}) unexpected zero "
-        + "bytes were found in the ND2 file and removed to allow further parsing."
-    )
-    for i in range(len(byte_ids)):
-        del image_group_data[byte_ids[i] : (byte_ids[i] + bytes_per_row)]
-
-
 def remove_parsed_unwanted_bytes(image_group_data, image_data_start, height, width):
     # Stitched ND2 files have been reported to contain unexpected (according to
     # image shape) zero bytes at the end of each image data row. This hinders
@@ -44,11 +33,6 @@ def remove_parsed_unwanted_bytes(image_group_data, image_data_start, height, wid
         image_group_data, image_data_start, height, width
     )
     if 0 != len(unwanted_byte_ids):
-        assert np.all(
-            image_group_data[unwanted_byte_ids + np.arange(len(unwanted_byte_ids))] == 0
-        ), (
-            f"{len(unwanted_byte_ids)} unexpected non-zero bytes were found"
-            + " in the ND2 file, the file could not be parsed."
-        )
-        remove_bytes_by_id(unwanted_byte_ids, image_group_data, height)
+        image_group_data = np.delete(np.array(image_group_data), unwanted_byte_ids)
+
     return image_group_data

release.txt

@@ -1,4 +1,4 @@
-Update version in 'nd2reader/__init__.py' file
+Update version in 'setup.py' file
 
 Rebuild sphinx documentation
 

requirements.txt

@@ -1,4 +1,4 @@
-numpy>=1.9.2
+numpy>=1.14
 six>=1.4
 xmltodict>=0.9.2
-pims>=0.3.0
+pims>=0.3.0

setup.py

@@ -1,16 +1,18 @@
 from setuptools import setup
-from nd2reader import __version__ as VERSION
+
+VERSION = '3.3.0'
 
 if __name__ == '__main__':
     setup(
         name='nd2reader',
         packages=['nd2reader'],
         install_requires=[
-            'numpy>=1.6.2',
+            'numpy>=1.14',
             'six>=1.4',
             'xmltodict>=0.9.2',
             'pims>=0.3.0'
         ],
+        python_requires=">=3.6",
         version=VERSION,
         description='A tool for reading ND2 files produced by NIS Elements',
         author='Ruben Verweij',

sphinx/tutorial.md

@@ -1,119 +0,0 @@
-# Tutorial
-
-### Installation
-
-The package is available on PyPi. Install it using:
-
-```
-pip install nd2reader
-```
-
-If you don't already have the packages `numpy`, `pims`, `six` and `xmltodict`, they will be installed automatically if you use the `setup.py` script.
-`nd2reader` is an order of magnitude faster in Python 3. I recommend using it unless you have no other choice. Python 2.7 and Python >= 3.4 are supported.
-
-#### Installation via Conda Forge
-
-Installing `nd2reader` from the `conda-forge` channel can be achieved by adding `conda-forge` to your channels with:
-
-```
-conda config --add channels conda-forge
-```
-
-Once the `conda-forge` channel has been enabled, `nd2reader` can be installed with:
-
-```
-conda install nd2reader
-```
-
-It is possible to list all of the versions of `nd2reader` available on your platform with:
-
-```
-conda search nd2reader --channel conda-forge
-```
-
-### Opening ND2s
-
-`nd2reader` follows the [pims](https://github.com/soft-matter/pims) framework. To open a file and show the first frame:
-
-```python
-from nd2reader import ND2Reader
-import matplotlib.pyplot as plt
-
-with ND2Reader('my_directory/example.nd2') as images:
-  plt.imshow(images[0])
-```
-
-After opening the file, all `pims` features are supported. Please refer to the [pims documentation](http://soft-matter.github.io/pims/).
-
-### ND2 metadata
-
-The ND2 file contains various metadata, such as acquisition information,
-regions of interest and custom user comments. Most of this metadata is parsed
-and available in dictionary form. For example:
-
-```python
-from nd2reader import ND2Reader
-
-with ND2Reader('my_directory/example.nd2') as images:
-    # width and height of the image
-    print('%d x %d px' % (images.metadata['width'], images.metadata['height']))
-```
-
-All metadata properties are:
-
-* `width`: the width of the image in pixels
-* `height`: the height of the image in pixels
-* `date`: the date the image was taken 
-* `fields_of_view`: the fields of view in the image
-* `frames`: a list of all frame numbers
-* `z_levels`: the z levels in the image
-* `total_images_per_channel`: the number of images per color channel
-* `channels`: the color channels
-* `pixel_microns`: the amount of microns per pixel
-* `rois`: the regions of interest (ROIs) defined by the user
-* `experiment`: information about the nature and timings of the ND experiment
-
-### Iterating over fields of view
-
-Using `NDExperiments` in the Nikon software, it is possible to acquire images on different `(x, y)` positions. 
-This is referred to as different fields of view. Using this reader, the fields of view are on the `v` axis. 
-For example:
-```python
-from nd2reader import ND2Reader
-
-with ND2Reader('my_directory/example.nd2') as images:
-    # width and height of the image
-    print(images.metadata)
-```
-will output
-```python
-{'channels': ['BF100xoil-1x-R', 'BF+RITC'],
- 'date': datetime.datetime(2017, 10, 30, 14, 35, 18),
- 'experiment': {'description': 'ND Acquisition',
-  'loops': [{'duration': 0,
-    'sampling_interval': 0.0,
-    'start': 0,
-    'stimulation': False}]},
- 'fields_of_view': [0, 1],
- 'frames': [0],
- 'height': 1895,
- 'num_frames': 1,
- 'pixel_microns': 0.09214285714285715,
- 'total_images_per_channel': 6,
- 'width': 2368,
- 'z_levels': [0, 1, 2]}
-```
-for our example file. As you can see from the metadata, it has two fields of view. We can also look at the sizes of the axes:
-```python
-    print(images.sizes)
-```
-```python
-{'c': 2, 't': 1, 'v': 2, 'x': 2368, 'y': 1895, 'z': 3}
-```
-As you can see, the fields of view are listed on the `v` axis. It is therefore possible to loop over them like this:
-```python
-    images.iter_axes = 'v'
-    for fov in images:
-        print(fov) # Frame containing one field of view
-```
-For more information on axis bundling and iteration, refer to the [pims documentation](http://soft-matter.github.io/pims/v0.4/multidimensional.html#axes-bundling).

sphinx/tutorial.rst

@@ -0,0 +1,148 @@
+Tutorial
+========
+
+Installation
+~~~~~~~~~~~~
+
+The package is available on PyPi. Install it using:
+
+::
+
+    pip install nd2reader
+
+If you don't already have the packages ``numpy``, ``pims``, ``six`` and
+``xmltodict``, they will be installed automatically if you use the
+``setup.py`` script. ``nd2reader`` is an order of magnitude faster in
+Python 3. I recommend using it unless you have no other choice. Python
+2.7 and Python >= 3.4 are supported.
+
+Installation via Conda Forge
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Installing ``nd2reader`` from the ``conda-forge`` channel can be
+achieved by adding ``conda-forge`` to your channels with:
+
+::
+
+    conda config --add channels conda-forge
+
+Once the ``conda-forge`` channel has been enabled, ``nd2reader`` can be
+installed with:
+
+::
+
+    conda install nd2reader
+
+It is possible to list all of the versions of ``nd2reader`` available on
+your platform with:
+
+::
+
+    conda search nd2reader --channel conda-forge
+
+Opening ND2s
+~~~~~~~~~~~~
+
+``nd2reader`` follows the `pims <https://github.com/soft-matter/pims>`__
+framework. To open a file and show the first frame:
+
+.. code:: python
+
+    from nd2reader import ND2Reader
+    import matplotlib.pyplot as plt
+
+    with ND2Reader('my_directory/example.nd2') as images:
+      plt.imshow(images[0])
+
+After opening the file, all ``pims`` features are supported. Please
+refer to the `pims
+documentation <http://soft-matter.github.io/pims/>`__.
+
+ND2 metadata
+~~~~~~~~~~~~
+
+The ND2 file contains various metadata, such as acquisition information,
+regions of interest and custom user comments. Most of this metadata is
+parsed and available in dictionary form. For example:
+
+.. code:: python
+
+    from nd2reader import ND2Reader
+
+    with ND2Reader('my_directory/example.nd2') as images:
+        # width and height of the image
+        print('%d x %d px' % (images.metadata['width'], images.metadata['height']))
+
+All metadata properties are:
+
+-  ``width``: the width of the image in pixels
+-  ``height``: the height of the image in pixels
+-  ``date``: the date the image was taken
+-  ``fields_of_view``: the fields of view in the image
+-  ``frames``: a list of all frame numbers
+-  ``z_levels``: the z levels in the image
+-  ``total_images_per_channel``: the number of images per color channel
+-  ``channels``: the color channels
+-  ``pixel_microns``: the amount of microns per pixel
+-  ``rois``: the regions of interest (ROIs) defined by the user
+-  ``experiment``: information about the nature and timings of the ND
+   experiment
+
+Iterating over fields of view
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Using ``NDExperiments`` in the Nikon software, it is possible to acquire
+images on different ``(x, y)`` positions. This is referred to as
+different fields of view. Using this reader, the fields of view are on
+the ``v`` axis. For example:
+
+.. code:: python
+
+    from nd2reader import ND2Reader
+
+    with ND2Reader('my_directory/example.nd2') as images:
+        # width and height of the image
+        print(images.metadata)
+
+will output
+
+.. code:: python
+
+    {'channels': ['BF100xoil-1x-R', 'BF+RITC'],
+     'date': datetime.datetime(2017, 10, 30, 14, 35, 18),
+     'experiment': {'description': 'ND Acquisition',
+      'loops': [{'duration': 0,
+        'sampling_interval': 0.0,
+        'start': 0,
+        'stimulation': False}]},
+     'fields_of_view': [0, 1],
+     'frames': [0],
+     'height': 1895,
+     'num_frames': 1,
+     'pixel_microns': 0.09214285714285715,
+     'total_images_per_channel': 6,
+     'width': 2368,
+     'z_levels': [0, 1, 2]}
+
+for our example file. As you can see from the metadata, it has two
+fields of view. We can also look at the sizes of the axes:
+
+.. code:: python
+
+        print(images.sizes)
+
+.. code:: python
+
+    {'c': 2, 't': 1, 'v': 2, 'x': 2368, 'y': 1895, 'z': 3}
+
+As you can see, the fields of view are listed on the ``v`` axis. It is
+therefore possible to loop over them like this:
+
+.. code:: python
+
+        images.iter_axes = 'v'
+        for fov in images:
+            print(fov) # Frame containing one field of view
+
+For more information on axis bundling and iteration, refer to the `pims
+documentation <http://soft-matter.github.io/pims/v0.4/multidimensional.html#axes-bundling>`__.