PyOPIA 2.5.11__tar.gz → 2.5.13__tar.gz

{pyopia-2.5.11 → pyopia-2.5.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOPIA
-Version: 2.5.11
+Version: 2.5.13
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Home-page: https://github.com/sintef/pyopia
 Keywords: Ocean,Particles,Imaging,Measurement,Size distribution

pyopia-2.5.13/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = '2.5.13'

{pyopia-2.5.11 → pyopia-2.5.13}/pyopia/classify.py

@@ -5,7 +5,6 @@ Module containing tools for classifying particle ROIs
 import os
 import numpy as np
 import pandas as pd
-
 import logging
 logger = logging.getLogger()
 
@@ -77,6 +76,10 @@ class Classify():
         self.model_path = model_path
         self.load_model()
 
+        # Get config for image resizing from the model
+        _, self.img_height, self.img_width, _ = self.model.get_config()['layers'][0]['config']['batch_shape']
+        self.pad_to_aspect_ratio = getattr(self.model.layers[0], 'pad_to_aspect_ratio', False)
+
         # Enable this to perform whitebalance correction in the preprocessing step
         self.correct_whitebalance = False
 
@@ -134,7 +137,7 @@ class Classify():
             A particle ROI with range 0.-255., corrected and preprocessed, ready for prediction
         '''
 
-        whitebalanced = np.copy(img_input).astype(np.float64)
+        whitebalanced = img_input.astype(np.float64)
 
         # Do white-balance correction as a per-channel histogram shift
         if self.correct_whitebalance:
@@ -150,14 +153,10 @@ class Classify():
         # which loads images in 0-255 range
         img = keras.utils.img_to_array(whitebalanced * 255)
 
-        # Get config for image resizing from the model
-        _, img_height, img_width, _ = self.model.get_config()['layers'][0]['config']['batch_shape']
-        pad_to_aspect_ratio = getattr(self.model.layers[0], 'pad_to_aspect_ratio', False)
-
         # resize to match the dimentions expected by the network
-        img = tf.image.resize(img, [img_height, img_width],
+        img = tf.image.resize(img, [self.img_height, self.img_width],
                               method=tf.image.ResizeMethod.BILINEAR,
-                              preserve_aspect_ratio=pad_to_aspect_ratio)
+                              preserve_aspect_ratio=self.pad_to_aspect_ratio)
 
         img_array = tf.keras.utils.img_to_array(img)
         img_preprocessed = tf.expand_dims(img_array, 0)  # Create a batch

{pyopia-2.5.11 → pyopia-2.5.13}/pyopia/io.py

@@ -84,14 +84,21 @@ def write_stats(stats,
             existing_stats = load_stats(datafilename + '-STATS.nc')
             xstats = xarray.concat([existing_stats, xstats], 'index')
         elif not append:
+            # When appending, only store the last row in the image_stats DataFrame
             datafilename += ('-Image-D' +
                              str(xstats['timestamp'][0].values).replace('-', '').replace(':', '').replace('.', '-'))
+
         encoding = setup_xstats_encoding(xstats)
         xstats.to_netcdf(datafilename + '-STATS.nc', encoding=encoding, engine=NETCDF_ENGINE, format='NETCDF4')
 
         # 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)
+            if append:
+                ximage_stats = image_stats.to_xarray()
+            else:
+                ximage_stats = image_stats.loc[[image_stats.index[-1]], :].to_xarray()
+
+            ximage_stats.to_netcdf(datafilename + '-STATS.nc', group='image_stats', mode='a', engine=NETCDF_ENGINE)
 
 
 def setup_xstats_encoding(xstats, string_vars=['export name', 'holo_filename']):
@@ -330,7 +337,7 @@ def merge_and_save_mfdataset(path_to_data, prefix='*', overwrite_existing_partia
     num_chunks = int(np.ceil(num_files / chunk_size_used))
     filelist_chunks = [sorted_filelist[i*chunk_size_used:min(num_files, (i+1)*chunk_size_used)] for i in range(num_chunks)]
     infostr = f'Processing {num_chunks} partial file lists of {chunk_size_used} files each'
-    infostr += ', based on a total of {num_files} files.'
+    infostr += f', based on a total of {num_files} files.'
     logging.info(infostr)
 
     # Get config from first file in list

{pyopia-2.5.11 → pyopia-2.5.13}/pyopia/process.py

@@ -259,14 +259,12 @@ def extract_particles(imc, timestamp, Classification, region_properties,
     stats : DataFrame
         List of particle statistics for every particle, according to Partstats class
     '''
-    filenames = ['not_exported'] * len(region_properties)
+    num_rows = max(len(region_properties), 1)
+    filenames = ['not_exported'] * num_rows
 
     if Classification is not None:
         # pre-allocation
-        predictions = np.zeros((len(region_properties),
-                                len(Classification.class_labels)),
-                               dtype='float64')
-        predictions *= np.nan
+        predictions = np.nan * np.zeros((num_rows, len(Classification.class_labels)), dtype='float64')
 
     # obtain the original image filename from the timestamp
     filename = timestamp.strftime('D%Y%m%dT%H%M%S.%f')
@@ -292,8 +290,8 @@ def extract_particles(imc, timestamp, Classification, region_properties,
         HDF5File = None
 
     # pre-allocate some things
-    data = np.zeros((len(region_properties), len(propnames)), dtype=np.float64)
-    bboxes = np.zeros((len(region_properties), 4), dtype=np.float64)
+    data = np.nan * np.zeros((num_rows, len(propnames)), dtype=np.float64)
+    bboxes = np.nan * np.zeros((num_rows, 4), dtype=np.float64)
     nb_extractable_part = 0
 
     for i, el in enumerate(region_properties):
@@ -630,7 +628,7 @@ class CalculateImageStats():
         data['image_stats'].loc[data['timestamp'], 'saturation'] = image_saturation
 
         # Skip remaining calculations if no particles where found
-        if data['stats'].size == 0:
+        if data['stats'].dropna().size == 0:
             return data
 
         # Calculate D50, nc and vc stats

pyopia-2.5.11/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '2.5.11'