PyOPIA 2.5.12__tar.gz → 2.6.0__tar.gz

{pyopia-2.5.12 → pyopia-2.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOPIA
-Version: 2.5.12
+Version: 2.6.0
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Home-page: https://github.com/sintef/pyopia
 Keywords: Ocean,Particles,Imaging,Measurement,Size distribution

pyopia-2.6.0/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = '2.6.0'

{pyopia-2.5.12 → pyopia-2.6.0}/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-2.5.12 → pyopia-2.6.0}/pyopia/cli.py

@@ -139,7 +139,7 @@ def process(config_filename: str, num_chunks: int = 1):
 
         check_chunks(num_chunks, pipeline_config)
 
-        progress.console.print("[blue]OBTAIN FILE LIST")
+        progress.console.print("[blue]OBTAIN IMAGE LIST")
         raw_files = pyopia.pipeline.FilesToProcess(pipeline_config['general']['raw_files'])
         conf_corrbg = pipeline_config['steps'].get('correctbackground', dict())
         average_window = conf_corrbg.get('average_window', 0)

{pyopia-2.5.12 → pyopia-2.6.0}/pyopia/pipeline.py

@@ -331,26 +331,32 @@ class FilesToProcess:
     '''Build file list from glob pattern if specified.
     Create FilesToProcess.chunked_files is chunks specified
     File list from glob will be sorted.
+    If a filelist file is specified, load the list from there without sorting.
 
     Parameters
     ----------
     glob_pattern : str, optional
-        Glob pattern, by default None
+        Glob pattern, by default None. If it ends with .txt, interpret as a filelist file.
     '''
     def __init__(self, glob_pattern=None):
         self.files = None
         self.background_files = []
         self.chunked_files = []
         if glob_pattern is not None:
-            self.files = sorted(glob(glob_pattern))
+            # If a .txt file is specified, this indicates we should get the filelist from there
+            if glob_pattern.endswith('.txt'):
+                self.from_filelist_file(glob_pattern)
+            else:
+                self.files = sorted(glob(glob_pattern))
 
     def from_filelist_file(self, path_to_filelist):
         '''
         Initialize explicit list of files to process from a text file.
         The text file should contain one path to an image per line, which should be processed in order.
         '''
+        logger.info(f'Loading explicit image file list from file: {path_to_filelist}')
         with open(path_to_filelist, 'r') as fh:
-            self.files = list(fh.readlines())
+            self.files = [line.rstrip() for line in fh.readlines()]
 
     def to_filelist_file(self, path_to_filelist):
         '''Write file list to a txt file

pyopia-2.5.12/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '2.5.12'