PyOPIA 2.4.6__tar.gz → 2.5.0__tar.gz

{pyopia-2.4.6 → pyopia-2.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOPIA
-Version: 2.4.6
+Version: 2.5.0
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Home-page: https://github.com/sintef/pyopia
 Keywords: Ocean,Particles,Imaging,Measurement,Size distribution

pyopia-2.5.0/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = '2.5.0'

{pyopia-2.4.6 → pyopia-2.5.0}/pyopia/instrument/silcam.py

@@ -51,6 +51,117 @@ def load_mono8(filename):
     return img
 
 
+def load_bayer_rgb8(filename):
+    '''load an RG8 .bsilc file from disc and convert it to RGB image
+
+    Assumes 8-bit Bayer-RG (Red-Green) image in range 0-255
+
+    Parameters
+    ----------
+    filename : string
+        filename to load
+
+    Returns
+    -------
+    array
+        raw image float between 0-1
+    '''
+    img_bayer = np.load(filename, allow_pickle=False).astype(np.int16)
+
+    # Check the image dimension
+    image_shape = np.shape(img_bayer)
+    if len(image_shape) > 2:
+        if image_shape[2] == 1:
+            img_bayer = img_bayer[:, :, 0]
+        else:
+            raise RuntimeError('Invalid image dimension')
+
+    M, N = img_bayer.shape[:2]   # Number of pixels in image height and width
+    img_bayer_min, img_bayer_max = np.min(img_bayer), np.max(img_bayer)
+
+    # img is a reconstructed RGB image
+    img = np.zeros((M, N, 3), dtype=np.uint8)
+    img[0:M:2, 0:N:2, 0] = img_bayer[0:M:2, 0:N:2]  # Red pixels
+    img[0:M:2, 1:N:2, 1] = img_bayer[0:M:2, 1:N:2]  # Green pixels on the first row
+    img[1:M:2, 0:N:2, 1] = img_bayer[1:M:2, 0:N:2]  # Green pixels on the second row
+    img[1:M:2, 1:N:2, 2] = img_bayer[1:M:2, 1:N:2]  # Blue pixels
+
+    # Boundary pixels interpolation in the first and last rows
+    # ***Red pixels
+    img[0, 2:N-1:2, 1] = (img_bayer[1, 2:N-1:2] + img_bayer[0, 1:N-2:2] + img_bayer[0, 3:N:2] + 1) // 3  # Interpolated G
+    img[0, 2:N-1:2, 2] = (img_bayer[1, 1:N-2:2] + img_bayer[1, 3:N:2] + 1) // 2  # Interpolated B
+    # ***Green pixels (odd columns)
+    img[0, 1:N-2:2, 0] = (img_bayer[0, 0:N-3:2] + img_bayer[0, 2:N-1:2] + 1) // 2  # Interpolated R
+    img[0, 1:N-2:2, 2] = img_bayer[1, 1:N-2:2]  # Interpolated B
+    # ***Blue pixels
+    img[M-1, 1:N-2:2, 1] = (img_bayer[M-2, 1:N-2:2]
+                            + img_bayer[M-1, 0:N-3:2] + img_bayer[M-1, 2:N-1:2] + 1) // 3  # Interpolated G
+    img[M-1, 1:N-2:2, 0] = (img_bayer[M-2, 0:N-3:2] + img_bayer[M-2, 2:N-1:2] + 1) // 2  # Interpolated R
+    # ***Green pixels (even columns)
+    img[M-1, 2:N-1:2, 2] = (img_bayer[M-1, 1:N-2:2] + img_bayer[M-1, 3:N:2] + 1) // 2  # Interpolated B
+    img[M-1, 2:N-1:2, 0] = img_bayer[M-2, 2:N-1:2]  # Interpolated R
+
+    # Boundary pixels interpolation in the first and last cols
+    # ***Red pixels
+    img[2:M-1:2, 0, 1] = (img_bayer[3:M:2, 0] + img_bayer[1:M-2:2, 0] + img_bayer[2:M-1:2, 1] + 1) // 3  # Interpolated G
+    img[2:M-1:2, 0, 2] = (img_bayer[3:M:2, 1] + img_bayer[1:M-2:2, 1] + 1) // 2  # Interpolated B
+    # ***Green pixels (odd columns)
+    img[1:M-2:2, 0, 0] = (img_bayer[0:M-3:2, 0] + img_bayer[2:M-1:2, 0] + 1) // 2  # Interpolated R
+    img[1:M-2:2, 0, 2] = img_bayer[1:M-2:2, 1]  # Interpolated B
+    # ***Blue pixels
+    img[1:M-2:2, N-1, 1] = (img_bayer[0:M-3:2, N-1]
+                            + img_bayer[2:M-1:2, N-1] + img_bayer[1:M-2:2, N-2] + 1) // 3  # Interpolated G
+    img[1:M-2:2, N-1, 0] = (img_bayer[0:M-3:2, N-2] + img_bayer[2:M-1:2, N-2] + 1) // 2  # Interpolated R
+    # ***Green pixels (even columns)
+    img[2:M-1:2, N-1, 0] = img_bayer[2:M-1:2, N-2]  # Interpolated R
+    img[2:M-1:2, N-1, 2] = (img_bayer[1:M-2:2, N-1]+img_bayer[3:M:2, N-1] + 1)//2  # Interpolated B
+
+    # Corner pixels interpolation
+    # *** top-left
+    img[0, 0, 1] = (img_bayer[1, 0] + img_bayer[0, 1] + 1) // 2  # Interpolated G
+    img[0, 0, 2] = img_bayer[1, 1]  # Interpolated B
+    # *** top-right
+    img[0, N-1, 0] = img_bayer[0, N-2]  # Interpolated R
+    img[0, N-1, 2] = img_bayer[1, N-1]  # Interpolated B
+    # *** bottom-left
+    img[M-1, 0, 0] = img_bayer[M-2, 0]  # Interpolated R
+    img[M-1, 0, 2] = img_bayer[M-1, 1]  # Interpolated B
+    # *** bottom-right
+    img[M-1, N-1, 1] = (img_bayer[M-2, N-1] + img_bayer[M-1, N-2] + 1) // 2  # Interpolated G
+    img[M-1, N-1, 0] = img_bayer[M-2, N-2]  # Interpolated R
+
+    # Internal pixels interpolation
+    # ***G pixel on odd row, even column
+    img[1:M-2:2, 2:N-1:2, 0] = (img_bayer[0:M-3:2, 2:N-1:2] + img_bayer[2:M-1:2, 2:N-1:2] + 1) // 2  # Interpolated R
+    img[1:M-2:2, 2:N-1:2, 2] = (img_bayer[1:M-2:2, 1:N-2:2] + img_bayer[1:M-2:2, 3:N:2] + 1) // 2  # Interpolated B
+    # ***G pixel on even row, odd column
+    img[2:M-1:2, 1:N-2:2, 0] = (img_bayer[2:M-1:2, 0:N-3:2] + img_bayer[2:M-1:2, 2:N-1:2] + 1) // 2  # Interpolated R
+    img[2:M-1:2, 1:N-2:2, 2] = (img_bayer[1:M-2:2, 1:N-2:2] + img_bayer[3:M:2, 1:N-2:2] + 1) // 2  # Interpolated B
+    # ***R pixel
+    img[2:M-1:2, 2:N-1:2, 1] = (img_bayer[1:M-2:2, 2:N-1:2]
+                                + img_bayer[3:M:2, 2:N-1:2] + img_bayer[2:M-1:2, 1:N-2:2]
+                                + img_bayer[2:M-1:2, 3:N:2] + 2) // 4  # Interpolated G
+    img[2:M-1:2, 2:N-1:2, 2] = (img_bayer[1:M-2:2, 1:N-2:2]
+                                + img_bayer[3:M:2, 1:N-2:2] + img_bayer[3:M:2, 3:N:2]
+                                + img_bayer[1:M-2:2, 3:N:2] + 2) // 4  # Interpolated B
+    # ***B pixel
+    img[1:M-2:2, 1:N-2:2, 0] = (img_bayer[0:M-3:2, 0:N-3:2]
+                                + img_bayer[2:M-1:2, 0:N-3:2] + img_bayer[2:M-1:2, 2:N-1:2]
+                                + img_bayer[0:M-3:2, 2:N-1:2] + 2) // 4  # Interpolated R
+    img[1:M-2:2, 1:N-2:2, 1] = (img_bayer[0:M-3:2, 1:N-2:2]
+                                + img_bayer[2:M-1:2, 1:N-2:2] + img_bayer[1:M-2:2, 0:N-3:2]
+                                + img_bayer[1:M-2:2, 2:N-1:2] + 2) // 4  # Interpolated G
+    img_min, img_max = np.min(img), np.max(img)
+
+    if img_min < 0 or img_max > 255 or (img_max - img_bayer_max) != 0 or (img_min - img_bayer_min) != 0:
+        raise ValueError(
+            "The converted RGB image is not suitable for further analysis. Check the pixel intensity ranges of the input image."
+            )
+
+    img = img.astype(np.float64) / 255
+    return img
+
+
 def load_rgb8(filename):
     '''load an RGB .silc file from disc
 
@@ -102,13 +213,14 @@ class SilCamLoad():
     Parameters
     ----------
     image_format : str, optional
-        Image file format. Can be either 'infer', 'rgb8' or 'mono8', by default 'infer'.
+        Image file format. Can be either 'infer', 'rgb8', 'bayer_rg8' or 'mono8', by default 'infer'.
 
     Note
     ----
         'infer' uses the file extension to determine the image format using the following convention:
          - '.silc' for RGB8
          - '.msilc' for MONO8
+         - '.bsilc' for BAYER_RG8
          - '.bmp' for using skimage.io.imread
 
     Returns
@@ -125,9 +237,10 @@ class SilCamLoad():
         self.image_format = image_format
         self.extension_load = {'.silc': load_rgb8,
                                '.msilc': load_mono8,
+                               '.bsilc': load_bayer_rgb8,
                                '.bmp': skimage.io.imread}
         self.format_load = {'RGB8': load_rgb8,
-                            'MONO8': load_mono8}
+                            'MONO8': load_mono8, 'BAYER_RG8': load_bayer_rgb8}
 
     def __call__(self, data):
         data['timestamp'] = timestamp_from_filename(data['filename'])

{pyopia-2.4.6 → pyopia-2.5.0}/pyopia/io.py

@@ -85,14 +85,39 @@ def write_stats(stats,
         elif not append:
             datafilename += ('-Image-D' +
                              str(xstats['timestamp'][0].values).replace('-', '').replace(':', '').replace('.', '-'))
-        encoding = {k: {'dtype': 'str'} for k in ['export name', 'holo_filename'] if k in xstats.data_vars}
+        encoding = setup_xstats_encoding(xstats)
         xstats.to_netcdf(datafilename + '-STATS.nc', encoding=encoding, engine=NETCDF_ENGINE, format='NETCDF4')
 
-        # If we have image statistics, add this to a group
+        # If we have image statistics (summary data for each raw image), add the image_stats a group
         if image_stats is not None:
             image_stats.to_xarray().to_netcdf(datafilename + '-STATS.nc', group='image_stats', mode='a', engine=NETCDF_ENGINE)
 
 
+def setup_xstats_encoding(xstats, string_vars=['export name', 'holo_filename']):
+    '''Setup encoding for writing to NetCDF, where string variables are explicitly defined as string types
+
+    Notes
+    -----
+    Setting up encoding like this for xstats is needed because default behaviour is to set everything as float if there is no
+    value, so in a situation where the first image contains no particles we must ensure that string variables are set as string
+    types.
+
+    Parameters
+    ----------
+    xstats : xarray.Dataset
+        Xarray version of stats dataframe, including metadata
+    string_vars : list, optional
+        list of string columns in xstats, by default ['export name', 'holo_filename']
+
+    Returns
+    -------
+    encoding : dict
+        'encoding' input argument to be given to xstats.to_netcdf()
+    '''
+    encoding = {k: {'dtype': 'str'} for k in string_vars if k in xstats.data_vars}
+    return encoding
+
+
 def make_xstats(stats, toml_steps):
     '''Converts a stats dataframe into xarray DataSet, with metadata
 
@@ -225,10 +250,12 @@ def merge_and_save_mfdataset(path_to_data, prefix='*'):
     output_name = os.path.join(path_to_data, prefix_out)
 
     logging.info(f'writing {output_name}')
-    write_stats(xstats,
-                output_name,
-                settings,
-                image_stats=image_stats)
+    # save the particle statistics (xstats) to NetCDF
+    encoding = setup_xstats_encoding(xstats)
+    xstats.to_netcdf(output_name + '-STATS.nc', encoding=encoding, engine=NETCDF_ENGINE, format='NETCDF4')
+    # if summary data for each raw image are available (image_stats), save this into the image_stats group
+    if image_stats is not None:
+        image_stats.to_netcdf(output_name + '-STATS.nc', group='image_stats', mode='a', engine=NETCDF_ENGINE)
     logging.info(f'writing {output_name} done.')
 
 

pyopia-2.4.6/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '2.4.6'