PyOPIA 2.4.7__tar.gz → 2.5.1__tar.gz

{pyopia-2.4.7 → pyopia-2.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOPIA
-Version: 2.4.7
+Version: 2.5.1
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Home-page: https://github.com/sintef/pyopia
 Keywords: Ocean,Particles,Imaging,Measurement,Size distribution

pyopia-2.5.1/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = '2.5.1'

{pyopia-2.4.7 → pyopia-2.5.1}/pyopia/instrument/holo.py

@@ -1,5 +1,15 @@
 '''
-Module containing hologram specific tools to enable compatability with the :mod:`pyopia.pipeline`
+This is a module containing basic processing for reconstruction of in-line holographic images with :mod:`pyopia.pipeline`.
+
+See (and references therein):
+Davies EJ, Buscombe D, Graham GW & Nimmo-Smith WAM (2015)
+'Evaluating Unsupervised Methods to Size and Classify Suspended Particles
+Using Digital In-Line Holography'
+Journal of Atmospheric and Oceanic Technology 32, (6) 1241-1256,
+https://doi.org/10.1175/JTECH-D-14-00157.1
+https://journals.ametsoc.org/view/journals/atot/32/6/jtech-d-14-00157_1.xml
+
+2022-11-01 Alex Nimmo-Smith alex.nimmo.smith@plymouth.ac.uk
 '''
 
 import os
@@ -17,20 +27,6 @@ from glob import glob
 import logging
 logger = logging.getLogger()
 
-'''
-This is a module containing basic processing for reconstruction of in-line holographic images.
-
-See (and references therein):
-Davies EJ, Buscombe D, Graham GW & Nimmo-Smith WAM (2015)
-'Evaluating Unsupervised Methods to Size and Classify Suspended Particles
-Using Digital In-Line Holography'
-Journal of Atmospheric and Oceanic Technology 32, (6) 1241-1256,
-https://doi.org/10.1175/JTECH-D-14-00157.1
-https://journals.ametsoc.org/view/journals/atot/32/6/jtech-d-14-00157_1.xml
-
-2022-11-01 Alex Nimmo-Smith alex.nimmo.smith@plymouth.ac.uk
-'''
-
 
 class Initial():
     '''PyOpia pipline-compatible class for one-time setup of holograhic reconstruction
@@ -472,7 +468,7 @@ class Focus():
 
     Returns
     -------
-    :class:`pyopia.pipeline.Data`
+    data : :class:`pyopia.pipeline.Data`
 
         containing the following keys:
 
@@ -547,11 +543,12 @@ class MergeStats():
 
     Parameters
     ----------
+    None
 
     Returns
     -------
-    updated stats
-
+    data : :class:`pyopia.pipeline.Data`
+        Updated pipeline data, where data['stats'] includes the new columns: 'holo_filename', 'z', and 'ifocus'
     '''
 
     def __init__(self):
@@ -573,6 +570,10 @@ class MergeStats():
             ifocus.append(stack_ifocus[np.argmin(total_diff)])
 
         stats['ifocus'] = np.array(ifocus, dtype=np.int64)
+        z = (np.arange(data['settings']['steps']['initial']['minZ'],
+                       (data['settings']['steps']['initial']['maxZ'] + data['settings']['steps']['initial']['stepZ']),
+                       data['settings']['steps']['initial']['stepZ']))
+        stats['z'] = z[stats['ifocus']-1]
         stats['holo_filename'] = data['filename']
         data['stats'] = stats
         return data

{pyopia-2.4.7 → pyopia-2.5.1}/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-2.4.7/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '2.4.7'