Merge pull request #1 from CellProfiler/acquisition_date

Include latests commits

Author: hackermd

.coveragerc

@@ -0,0 +1,18 @@
+[run]
+branch = True
+erase = True
+package = bioformats
+[report]
+exclude_lines =
+    # Ignore continue statement in code as it can't be detected as covered
+    # due to an optimization by the Python interpreter. See coverage issue
+    # ( https://bitbucket.org/ned/coveragepy/issue/198/continue-marked-as-not-covered )
+    # and Python issue ( http://bugs.python.org/issue2506 ).
+    continue
+
+    # Ignore coverage of code that requires the module to be executed.
+    if __name__ == .__main__.:
+omit =
+    */python?.?/*
+    */site-packages/*
+    *tests/*

.travis.yml

@@ -0,0 +1,51 @@
+language: java
+env:
+   - PYTHON_VERSION="2.7"
+before_install:
+   # Get the tag if it wasn't provided. Travis doesn't provide this if it isn't a tagged build.
+   - if [ -z $TRAVIS_TAG ]; then TRAVIS_TAG=`git tag --contains` ; fi
+   - echo $TRAVIS_TAG
+   # Move out of git directory to build root.
+   - cd ../..
+   - pwd
+install:
+   # Download and configure conda.
+   - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+   - bash miniconda.sh -b -p $HOME/miniconda
+   - export PATH="$HOME/miniconda/bin:$PATH"
+   - conda config --set always_yes yes
+   - conda config --set show_channel_urls True
+   - source activate root
+   # Install basic conda dependencies.
+   - touch $HOME/miniconda/conda-meta/pinned
+   - echo "conda-build ==1.16.0" >> $HOME/miniconda/conda-meta/pinned
+   - conda update --all
+   - conda install conda-build
+   # Setup environment for testing and install all dependencies and our package.
+   - cd $TRAVIS_REPO_SLUG
+   - conda create --use-local -n testenv python=$PYTHON_VERSION
+   - source activate testenv
+   - conda install numpy
+   - python setup.py install
+   # Install sphinx to build documentation.
+   - conda install sphinx
+   # Install coverage and coveralls to generate and submit test coverage results for coveralls.io.
+   - echo "coverage 3.*" >> $HOME/miniconda/envs/testenv/conda-meta/pinned
+   - conda install nose
+   - conda install coverage
+   - pip install coveralls
+   # Clean up downloads as there are quite a few and they waste space/memory.
+   - conda clean -tipsy
+   - rm -rfv $HOME/.cache/pip
+script:
+   # Run tests.
+   - python nosetests.py
+   # Build docs.
+   - cd docs
+   - make html
+   - cd ..
+#after_success:
+   # Submit results to coveralls.io.
+   #- coveralls
+# Use container format for TravisCI for quicker startup and builds.
+sudo: false

README.rst

@@ -1,3 +1,7 @@
+|Travis CI Status|
+
+-----------------------------------------------------------------------------------------------------
+
 Python-bioformats is a Python wrapper for Bio-Formats, a standalone
 Java library for reading and writing life sciences image file
 formats. Bio-Formats is capable of parsing both pixels and metadata
@@ -20,3 +24,7 @@ python-bioformats is licensed under the GNU General Public License
 See the accompanying files COPYING and LICENSE for details.
 
 Copyright (c) 2009-2014 Broad Institute. All rights reserved.
+
+
+.. |Travis CI Status| image:: https://travis-ci.org/CellProfiler/python-bioformats.svg?branch=master
+   :target: https://travis-ci.org/CellProfiler/python-bioformats

bioformats/formatwriter.py

@@ -59,11 +59,11 @@ def write_image(pathname, pixels, pixel_type,
         
     :param t: the image's `t` index
         
-    :param sizeC: # of channels in the stack
+    :param size_c: # of channels in the stack
         
-    :param sizeZ: # of z stacks
+    :param size_z: # of z stacks
         
-    :param sizeT: # of timepoints in the stack
+    :param size_t: # of timepoints in the stack
         
     :param channel_names: names of the channels (make up names if not present).
 

bioformats/tests/test_omexml.py

@@ -46,13 +46,13 @@ def test_02_01_iter_children(self):
     def test_02_02_get_text(self):
         o = O.OMEXML(TIFF_XML)
         ad = o.root_node.find(
-            "/".join([O.qn(o.get_ns('ome'), x) for x in ("Image", "AcquiredDate")]))
+            "/".join([O.qn(o.get_ns('ome'), x) for x in ("Image", "AcquisitionDate")]))
         self.assertEqual(O.get_text(ad), "2008-02-05T17:24:46")
 
     def test_02_04_set_text(self):
         o = O.OMEXML(TIFF_XML)
         ad = o.root_node.find("/".join(
-            [O.qn(o.get_ns('ome'), x) for x in ("Image", "AcquiredDate")]))
+            [O.qn(o.get_ns('ome'), x) for x in ("Image", "AcquisitionDate")]))
         im = o.root_node.find(O.qn(o.get_ns("ome"), "Image"))
         O.set_text(im, "Foo")
         self.assertEqual(O.get_text(im), "Foo")
@@ -99,14 +99,25 @@ def test_04_04_image_set_name(self):
         o.image(0).Name = "Foo"
         self.assertEquals(o.image(0).node.get("Name"), "Foo")
 
-    def test_04_05_image_get_acquired_date(self):
+    def test_04_05_image_get_acquisition_date(self):
         o = O.OMEXML(TIFF_XML)
-        self.assertEqual(o.image(0).AcquiredDate, "2008-02-05T17:24:46")
+        self.assertEqual(o.image(0).AcquisitionDate, "2008-02-05T17:24:46")
 
-    def test_04_06_image_set_acquired_date(self):
+    def test_04_06_image_set_acquisition_date(self):
         o = O.OMEXML(TIFF_XML)
-        o.image(0).AcquiredDate = "2011-12-21T11:04:14.903000"
-        self.assertEqual(o.image(0).AcquiredDate, "2011-12-21T11:04:14.903000")
+        o.image(0).AcquisitionDate = "2011-12-21T11:04:14.903000"
+        self.assertEqual(o.image(0).AcquisitionDate, "2011-12-21T11:04:14.903000")
+        
+    def test_04_07_image_1_acquisition_date(self):
+        # regression test of #38
+        o = O.OMEXML()
+        o.set_image_count(2)
+        date_1 = "2011-12-21T11:04:14.903000"
+        date_2 = "2015-10-13T09:57:00.000000"
+        o.image(0).AcquisitionDate = date_1
+        o.image(1).AcquisitionDate = date_2
+        self.assertEqual(o.image(0).AcquisitionDate, date_1)
+        self.assertEqual(o.image(1).AcquisitionDate, date_2)
 
     def test_05_01_pixels_get_id(self):
         o = O.OMEXML(TIFF_XML)
@@ -736,7 +747,7 @@ def test_14_17_set_position_z(self):
 	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2013-06 http://www.openmicroscopy.org/Schemas/OME/2013-06/ome.xsd">
 	<Image ID="Image:0" Name="Channel1-01-A-01.tif">
-		<AcquiredDate>2008-02-05T17:24:46</AcquiredDate>
+		<AcquisitionDate>2008-02-05T17:24:46</AcquisitionDate>
 		<Pixels DimensionOrder="XYCZT" ID="Pixels:0" PhysicalSizeX="352.77777777777777"
 			PhysicalSizeY="352.77777777777777" SizeC="2" SizeT="3" SizeX="640"
 			SizeY="512" SizeZ="1" Type="uint8">

docs/index.rst

@@ -23,8 +23,9 @@ Installation and testing
 Install using pip
 -----------------
 
-    pip install python-bioformats
+::
 
+    pip install python-bioformats
 
 Running the unit tests
 ----------------------