Merge pull request #209 from micasense/fix-unit-tests

Add GitHub Actions and fix unit tests

.github/workflows/python-test.yml

@@ -0,0 +1,47 @@
+name: Build and run Python unit tests
+
+on: push
+permissions:
+  contents: read
+jobs:
+  test-linux:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.8'
+      - name: Add system deps and exiftool
+        run: |
+          sudo apt-get update
+          sudo apt-get install libzbar0 make perl
+          wget https://cpan.metacpan.org/authors/id/E/EX/EXIFTOOL/Image-ExifTool-12.76.tar.gz
+          tar -xzf Image-ExifTool-12.76.tar.gz
+          pushd Image-ExifTool-12.76/
+          perl Makefile.PL
+          make test
+          sudo make install
+          popd
+      - name: Add conda to system path
+        run: |
+          # $CONDA is an environment variable pointing to the root of the miniconda directory
+          echo $CONDA/bin >> $GITHUB_PATH
+      - name: Install dependencies
+        run: |
+          source "$CONDA/etc/profile.d/conda.sh"
+          hash -r
+          conda config --set always_yes yes --set changeps1 no
+          conda update -q conda
+          conda update -n base conda
+          conda info -a
+          conda env create -f micasense_conda_env.yml
+          conda activate micasense
+      - name: Test with pytest
+        run: |
+          source "$CONDA/etc/profile.d/conda.sh"
+          conda activate micasense
+          git lfs install
+          git lfs pull
+          pytest --junit-xml=test-results.xml

micasense/image.py

@@ -65,7 +65,7 @@ class Image(object):
     band of multispectral information
     """
 
-    def __init__(self, image_path, exiftool_obj=None, allow_uncalibrated=False):
+    def __init__(self, image_path: str, exiftool_obj=None, allow_uncalibrated=False):
         if not os.path.isfile(image_path):
             raise IOError("Provided path is not a file: {}".format(image_path))
         self.path = image_path
@@ -191,7 +191,7 @@ def compute_horizontal_irradiance_dls1(self):
         return self.horizontal_irradiance_from_direct_scattered()
 
     def compute_horizontal_irradiance_dls2(self):
-        """ Compute the proper solar elevation, solar azimuth, and horizontal irradiance 
+        """ Compute the proper solar elevation, solar azimuth, and horizontal irradiance
             for cases where the camera system did not do it correctly """
         _, _, _, \
             self.solar_elevation, \
@@ -373,7 +373,7 @@ def vignette(self):
             yv = y.T / y_dim
             k = self.vignette_polynomial2D
             e = self.vignette_polynomial2Dexponents
-            p2 = np.zeros_like(xv, dtype=np.float)
+            p2 = np.zeros_like(xv, dtype=float)
             for i, c in enumerate(k):
                 ex = e[2 * i]
                 ey = e[2 * i + 1]

micasense/imageset.py

@@ -67,7 +67,7 @@ def from_directory(cls, directory, progress_callback=None, exiftool_path=None, a
         if exiftool_path is None and os.environ.get('exiftoolpath') is not None:
             exiftool_path = os.path.normpath(os.environ.get('exiftoolpath'))
 
-        with exiftool.ExifTool(exiftool_path) as exift:
+        with exiftool.ExifToolHelper(exiftool_path) as exift:
             for i, path in enumerate(matches):
                 images.append(image.Image(path, exiftool_obj=exift, allow_uncalibrated=allow_uncalibrated))
                 if progress_callback is not None:

micasense/imageutils.py

@@ -509,7 +509,7 @@ def min_max(pts):
 
 def map_points(pts, image_size, warpMatrix, distortion_coeffs, camera_matrix, warp_mode=cv2.MOTION_HOMOGRAPHY):
     # extra dimension makes opencv happy
-    pts = np.array([pts], dtype=np.float)
+    pts = np.array([pts], dtype=float)
     new_cam_mat, _ = cv2.getOptimalNewCameraMatrix(camera_matrix, distortion_coeffs, image_size, 1)
     new_pts = cv2.undistortPoints(pts, camera_matrix, distortion_coeffs, P=new_cam_mat)
     if warp_mode == cv2.MOTION_AFFINE:
@@ -584,7 +584,7 @@ def radiometric_pan_sharpen(capture, warp_matrices=None, panchro_band=5, irradia
     # this function performs a radiometrically accurate pansharpening on the input capture
     # if no warp matrices are supplied to align the multispec images to the pan band
     # the camera calibration is used (which produces reasonably well aligned imagers in most cases)
-    # in addition to the pan sharpened stack, the equivalent upsampled stack is also produced 
+    # in addition to the pan sharpened stack, the equivalent upsampled stack is also produced
     # for comparison
     # use the warp matrices we have for the stack, if not user supplied
     if warp_matrices is None:
@@ -654,9 +654,9 @@ def radiometric_pan_sharpen(capture, warp_matrices=None, panchro_band=5, irradia
 def prepare_exif_for_stacks(thecapture, thefilename):
     lat, lon, alt = thecapture.location()
     resolution = thecapture.images[0].focal_plane_resolution_px_per_mm
-    # eventually it would be nice to add the capture ID, flight ID, 
+    # eventually it would be nice to add the capture ID, flight ID,
     # and yaw/pitch/roll, but these are non-standard exif tags,
-    # so it is more difficult. 
+    # so it is more difficult.
     attitude = thecapture.dls_pose()
     theid = thecapture.uuid
     flightid = thecapture.flightid

micasense/metadata.py

@@ -36,7 +36,7 @@
 class Metadata(object):
     """ Container for Micasense image metadata"""
 
-    def __init__(self, filename, exiftool_path=None, exiftool_obj=None):
+    def __init__(self, filename: str, exiftool_path=None, exiftool_obj=None):
         if exiftool_obj is not None:
             self.exif = exiftool_obj.get_metadata(filename)
             return
@@ -48,7 +48,7 @@ def __init__(self, filename, exiftool_path=None, exiftool_obj=None):
             self.exiftoolPath = None
         if not os.path.isfile(filename):
             raise IOError("Input path is not a file")
-        with exiftool.ExifTool(self.exiftoolPath) as exift:
+        with exiftool.ExifToolHelper() as exift:
             self.exif = exift.get_metadata(filename)
 
     def get_all(self):
@@ -59,10 +59,11 @@ def get_item(self, item, index=None):
         """ Get metadata item by Namespace:Parameter"""
         val = None
         try:
-            val = self.exif[item]
+            assert len(self.exif) > 0
+            val = self.exif[0][item]
             if index is not None:
                 try:
-                    if isinstance(val, unicode):
+                    if isinstance(val, pytz.unicode):
                         val = val.encode('ascii', 'ignore')
                 except NameError:
                     # throws on python 3 where unicode is undefined
@@ -83,7 +84,7 @@ def size(self, item):
         """get the size (length) of a metadata item"""
         val = self.get_item(item)
         try:
-            if isinstance(val, unicode):
+            if isinstance(val, pytz.unicode):
                 val = val.encode('ascii', 'ignore')
         except NameError:
             # throws on python 3 where unicode is undefined
@@ -132,7 +133,6 @@ def utc_time(self):
             if subsec < 0:
                 negative = -1.0
                 subsec *= -1.0
-            subsec = float('0.{}'.format(int(subsec)))
             subsec *= negative
             ms = subsec * 1e3
             utc_time += timedelta(milliseconds=ms)
@@ -336,7 +336,7 @@ def horizontal_irradiance_valid(self):
         return version.parse(version_string) >= version.parse(good_version)
 
     def spectral_irradiance(self):
-        """ Raw spectral irradiance measured by an irradiance sensor. 
+        """ Raw spectral irradiance measured by an irradiance sensor.
             Calibrated to W/m^2/nm using irradiance_scale_factor, but not corrected for angles """
         return self.__float_or_zero(self.get_item('XMP:SpectralIrradiance')) * self.irradiance_scale_factor()
 
@@ -379,7 +379,7 @@ def auto_calibration_image(self):
             self.panel_serial() is not None
 
     def panel_albedo(self):
-        """ Surface albedo of the active portion of the reflectance panel as calculated by the camera 
+        """ Surface albedo of the active portion of the reflectance panel as calculated by the camera
             (usually from the information in the panel QR code) """
         albedo = self.get_item('XMP:Albedo')
         if albedo is not None:

micasense/utils.py

@@ -128,10 +128,10 @@ def correct_lens_distortion(meta, image):
     ndistortion = meta.size('XMP:PerspectiveDistortion')
     distortion_parameters = np.array([float(meta.get_item('XMP:PerspectiveDistortion', i)) for i in range(ndistortion)])
     # get the two principal points
-    pp = np.array(meta.get_item('XMP:PrincipalPoint').split(',')).astype(np.float)
+    pp = np.array(meta.get_item('XMP:PrincipalPoint').split(',')).astype(float)
     # values in pp are in [mm] and need to be rescaled to pixels
-    focal_plane_x_resolution = float(meta.get_item('EXIF:focal_plane_x_resolution'))
-    focal_plane_y_resolution = float(meta.get_item('EXIF:focal_plane_y_resolution'))
+    focal_plane_x_resolution = float(meta.get_item('EXIF:FocalPlaneXResolution'))
+    focal_plane_y_resolution = float(meta.get_item('EXIF:FocalPlaneYResolution'))
 
     cX = pp[0] * focal_plane_x_resolution
     cY = pp[1] * focal_plane_y_resolution