Merge branch 'master' into enh/set_dim

Author: jgrewe

.github/workflows/pythonpackage.yml

@@ -37,7 +37,7 @@ jobs:
         pylint --rcfile=.pylintrc nixio
     - name: Test with pytest
       run: |
-        pip install pytest
+        pip install pytest scipy pillow matplotlib
         # pytest will skip cross-compatibility tests since NIX isn't installed
         pytest
 
@@ -69,7 +69,7 @@ jobs:
       - name: Install Python dependencies
         run: |
           python setup.py install
-          pip install pytest
+          pip install pytest scipy pillow matplotlib
       - name: Run tests
         run: |
           pytest
@@ -86,7 +86,7 @@ jobs:
       - name: Install dependencies
         run: |
           python setup.py install
-          pip install pytest coveralls
+          pip install pytest coveralls scipy pillow matplotlib
       - name: Create coverage
         run: |
           coverage run --source=nixio -m pytest nixio/test/
@@ -107,7 +107,7 @@ jobs:
       - name: Install dependencies
         run: |
           python setup.py install
-          pip install pytest pytest-cov
+          pip install pytest pytest-cov scipy pillow matplotlib
       - name: Create coverage
         run: |
           pytest --cov=./ --cov-report=xml

appveyor.yml

@@ -60,7 +60,7 @@ install:
   # - cd ..
   - python -m pip install certifi
   - python -m pip install -U pip wheel
-  - python -m pip install numpy h5py pytest-xdist
+  - python -m pip install numpy h5py pytest-xdist scipy pillow matplotlib
   - ps: cd "$env:APPVEYOR_BUILD_FOLDER"
   - set DISTUTILS_USE_SDK="1"
   - set MSSdk="1"

docs/source/examples/imageData.py

@@ -38,8 +38,8 @@ def load_image():
 
 
 def plot_data(data_array):
-    img_data = np.zeros(data_array.data.shape)
-    data_array.data.read_direct(img_data)
+    img_data = np.zeros(data_array.shape)
+    data_array.read_direct(img_data)
     img_data = np.array(img_data, dtype='uint8')
     new_img = img.fromarray(img_data)
     new_img.show()

docs/source/examples/imageWithMetadata.py

@@ -35,7 +35,7 @@ def print_metadata_table(section, ax):
     cell_text = []
     for p in section.items():
         for i, v in enumerate(p[1].values):
-            value = str(v.value)
+            value = str(v)
             if len(value) > 30:
                 value = value[:30] + '...'
             if i == 0:
@@ -63,8 +63,8 @@ def load_image():
 
 
 def plot_data(data_array):
-    img_data = np.zeros(data_array.data.shape)
-    data_array.data.read_direct(img_data)
+    img_data = np.zeros(data_array.shape)
+    data_array.read_direct(img_data)
     img_data = np.array(img_data, dtype='uint8')
     new_img = img.fromarray(img_data)
 

docs/source/examples/multipleTimeSeries.py

@@ -29,10 +29,10 @@ def create_data(duration=1, freq=10, stepsize=0.01):
 def plot_data(data_array):
     set_dim = data_array.dimensions[0]
     x_axis = data_array.dimensions[1]
-    x = np.arange(0, data_array.data.shape[1])
+    x = np.arange(0, data_array.shape[1])
     x = x * x_axis.sampling_interval + x_axis.offset
-    y = np.zeros(data_array.data.shape)
-    data_array.data.read_direct(y)
+    y = np.zeros(data_array.shape)
+    data_array.read_direct(y)
     for i, label in enumerate(set_dim.labels):
         plt.plot(x, y[i, :], label=label)
 

docs/source/examples/regularlySampledData.py

@@ -27,8 +27,8 @@ def create_sinewave(duration=1, freq=10, stepsize=0.01):
 
 def plot_data(data_array):
     x_axis = data_array.dimensions[0]
-    x = x_axis.axis(data_array.data.shape[0])
-    y = data_array.data[:]
+    x = x_axis.axis(data_array.shape[0])
+    y = data_array[:]
 
     plt.plot(x, y, marker=".", markersize=5, label=data_array.name)
     plt.xlabel(x_axis.label + " [" + x_axis.unit + "]")

docs/source/examples/singleROI.py

@@ -43,16 +43,16 @@ def draw_rect(img_data, position, extent):
 
 def plot_data(tag):
     data_array = tag.references[0]
-    img_data = np.zeros(data_array.data.shape)
-    data_array.data.read_direct(img_data)
+    img_data = np.zeros(data_array.shape)
+    data_array.read_direct(img_data)
     img_data = np.array(img_data, dtype='uint8')
     # positions and extents are double by default, need to convert to int
     pos = tuple(map(int, tag.position))
     ext = tuple(map(int, tag.extent))
     draw_rect(img_data, pos, ext)
     new_img = img.fromarray(img_data)
 
-    new_img.save("../images/single_roi.png")
+    # new_img.save("../images/single_roi.png")
     new_img.show()
 
 

docs/source/examples/spikeFeatures.py

@@ -47,8 +47,8 @@ def fake_neuron(stepsize=0.001, offset=.8, sta_offset=1000):
 
 def plot_data(tag):
     data_array = tag.references[0]
-    voltage = np.zeros(data_array.data.shape)
-    data_array.data.read_direct(voltage)
+    voltage = np.zeros(data_array.shape)
+    data_array.read_direct(voltage)
 
     x_axis = data_array.dimensions[0]
     time = x_axis.axis(data_array.data_extent[0])

docs/source/examples/spikeTagging.py

@@ -29,14 +29,14 @@ def fake_neuron():
 
 def plot_data(tag):
     data_array = tag.references[0]
-    voltage = np.zeros(data_array.data.shape)
-    data_array.data.read_direct(voltage)
+    voltage = np.zeros(data_array.shape)
+    data_array.read_direct(voltage)
 
     x_axis = data_array.dimensions[0]
-    time = x_axis.axis(data_array.data.shape[0])
+    time = x_axis.axis(data_array.shape[0])
 
     spike_times = np.zeros(tag.positions.data_extent)
-    tag.positions.data.read_direct(spike_times)
+    tag.positions.read_direct(spike_times)
 
     fig = plt.figure(figsize=(5.5, 2.5))
     ax = fig.add_subplot(111)
@@ -48,7 +48,7 @@ def plot_data(tag):
     ax.set_ylim((1.5 * np.min(voltage), 1.5 * np.max(voltage)))
     ax.legend()
     fig.subplots_adjust(bottom=0.175, top=0.975, right=0.975)
-    fig.savefig("../images/spike_tagging.png")
+    # fig.savefig("../images/spike_tagging.png")
     plt.show()
 
 

nixio/test/test_doc_examples.py

@@ -0,0 +1,180 @@
+import importlib.util as getmod
+import os
+import runpy
+import sys
+import unittest
+
+from pathlib import Path
+from shutil import copyfile
+
+import matplotlib.pyplot as plt
+
+
+TEST_IMAGE = "lenna.png"
+
+
+class TestDocumentationExamples(unittest.TestCase):
+
+    def run_script(self, script_name):
+        file_path = Path.joinpath(self.examples_path, script_name)
+        runpy.run_path(path_name=str(file_path), run_name="__main__")
+
+    def handle_lif(self):
+        lif_path = Path.joinpath(self.examples_path, "lif.py")
+        spec = getmod.spec_from_file_location("lif", str(lif_path))
+        spec.loader.load_module("lif")
+
+    def handle_image(self):
+        image_path = Path.joinpath(self.examples_path, TEST_IMAGE)
+        copyfile(str(image_path), str(Path.joinpath(Path(os.getcwd()), TEST_IMAGE)))
+
+    def setUp(self):
+        curr_path = os.getcwd()
+        if os.path.basename(curr_path) == "nixpy":
+            self.examples_path = Path.joinpath(Path(curr_path),
+                                               "docs", "source", "examples")
+        elif os.path.basename(curr_path) == "nixio":
+            self.examples_path = Path.joinpath(Path(curr_path).parent,
+                                               "docs", "source", "examples")
+        elif os.path.basename(curr_path) == "test":
+            self.examples_path = Path.joinpath(Path(curr_path).parent.parent,
+                                               "docs", "source", "examples")
+
+        # Render matplotlib plots non-blocking
+        plt.ion()
+
+    def tearDown(self):
+        plt.close("all")
+        plt.ioff()
+        if os.path.exists(TEST_IMAGE):
+            os.remove(TEST_IMAGE)
+
+    def test_annotations(self):
+        self.run_script("annotations.py")
+        # cleanup
+        os.remove("annotations.nix")
+
+    def test_category_data(self):
+        self.run_script("categoryData.py")
+        # cleanup
+        os.remove("categoryData.nix")
+
+    def test_continuous_recording(self):
+        self.run_script("continuousRecording.py")
+        # cleanup
+        os.remove("continuous_recording.nix")
+
+    def test_file_create(self):
+        self.run_script("fileCreate.py")
+        # cleanup
+        os.remove("file_create_example.nix")
+
+    def test_image_data(self):
+        # test will open image with an external program; does not work on windows
+        if sys.platform == 'linux':
+            # Requires PIL package and the "Lenna" image.
+            self.handle_image()
+            self.run_script("imageData.py")
+            # cleanup
+            os.remove("image_example.nix")
+
+    def test_image_with_metadata(self):
+        # Requires PIL package and the "Lenna" image.
+        self.handle_image()
+        self.run_script("imageWithMetadata.py")
+        # cleanup
+        os.remove("image_with_source_example.h5")
+        os.remove("image_with_metadata.png")
+
+    def test_irregularly_sampled_data(self):
+        self.run_script("irregularlySampledData.py")
+        # cleanup
+        os.remove("irregular_data_example.nix")
+
+    def test_lif(self):
+        self.run_script("lif.py")
+
+    def test_multiple_points(self):
+        self.run_script("multiple_points.py")
+        # cleanup
+        os.remove("multiple_points.nix")
+
+    def test_multiple_regions(self):
+        self.run_script("multiple_regions.py")
+        # cleanup
+        os.remove("multiple_regions.nix")
+
+    def test_multiple_rois(self):
+        # Requires PIL package and the "Lenna" image.
+        self.handle_image()
+        self.run_script("multipleROIs.py")
+        # cleanup
+        os.remove("multiple_roi.nix")
+
+    def test_range_dimension_link(self):
+        self.run_script("rangeDimensionLink.py")
+        # cleanup
+        os.remove("range_link.nix")
+
+    def test_regularly_sampled_data(self):
+        self.run_script("regularlySampledData.py")
+        # cleanup
+        os.remove("regular_data_example.nix")
+
+    def test_single_roi(self):
+        # test will open image with an external program; does not work on windows
+        if sys.platform == 'linux':
+            # Requires PIL package and the "Lenna" image.
+            self.handle_image()
+            self.run_script("singleROI.py")
+            # cleanup
+            os.remove("single_roi.nix")
+
+    def test_sources(self):
+        self.run_script("sources.py")
+        # cleanup
+        os.remove("sources.nix")
+
+    def test_spike_features(self):
+        # Requires scipy package and "lif.py"
+        self.handle_lif()
+        self.run_script("spikeFeatures.py")
+        # cleanup
+        os.remove("spike_features.h5")
+
+    def test_spike_tagging(self):
+        # Requires "lif.py"
+        self.handle_lif()
+        self.run_script("spikeTagging.py")
+        # cleanup
+        os.remove("spike_tagging.nix")
+
+    def test_tabular_data(self):
+        self.run_script("tabulardata.py")
+        # cleanup
+        os.remove("dataframe.nix")
+
+    def test_tagged_feature(self):
+        # Requires scipy package and "lif.py"
+        self.handle_lif()
+        self.run_script("taggedFeature.py")
+        # cleanup
+        os.remove("spike_features.nix")
+
+    def test_tagging_example(self):
+        # Requires scipy package
+        self.run_script("tagging_example.py")
+        # cleanup
+        os.remove("tagging1.nix")
+
+    def test_tagging_nd(self):
+        # not testing any nix feature
+        # self.run_script("tagging_nd.py")
+        pass
+
+    def test_untagged_feature(self):
+        # Requires scipy package and "lif.py"
+        self.handle_lif()
+        self.run_script("untaggedFeature.py")
+        # cleanup
+        os.remove("untagged_feature.h5")