PyOPIA 2.8.0__tar.gz → 2.8.2__tar.gz

{pyopia-2.8.0 → pyopia-2.8.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOPIA
-Version: 2.8.0
+Version: 2.8.2
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Home-page: https://github.com/sintef/pyopia
 Keywords: Ocean,Particles,Imaging,Measurement,Size distribution
@@ -9,6 +9,7 @@ Author-email: emlyn.davies@sintef.no
 Requires-Python: >=3.12,<4.0
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Provides-Extra: classification
 Provides-Extra: classification-arm64
 Requires-Dist: cmocean (>=3.0.3,<4.0.0)

pyopia-2.8.2/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = '2.8.2'

{pyopia-2.8.0 → pyopia-2.8.2}/pyopia/cli.py

@@ -172,28 +172,13 @@ def process(config_filename: str, num_chunks: int = 1, strategy: str = 'block'):
 
         progress.console.print("[blue]INITIALISE PIPELINE")
 
-    def process_file_list(file_list, c):
-        processing_pipeline = pyopia.pipeline.Pipeline(pipeline_config)
-
-        with get_custom_progress_bar(f'[blue]Processing progress (chunk {c})', disable=c != 0) as pbar:
-            for filename in pbar.track(file_list, description=f'[blue]Processing progress (chunk {c})'):
-                try:
-                    logger.debug(f'Chunk {c} starting to process {filename}')
-                    processing_pipeline.run(filename)
-                except Exception as e:
-                    logger.warning('[red]An error occured in processing, ' +
-                                   'skipping rest of pipeline and moving to next image.' +
-                                   f'(chunk {c})')
-                    logger.error(e)
-                    logger.debug(''.join(traceback.format_tb(e.__traceback__)))
-
     # With one chunk we keep the non-multiprocess functionality to ensure backwards compatibility
     job_list = []
     if num_chunks == 1:
-        process_file_list(raw_files, 0)
+        process_file_list(raw_files, pipeline_config, 0)
     else:
         for c, chunk in enumerate(raw_files.chunked_files):
-            job = multiprocessing.Process(target=process_file_list, args=(chunk, c))
+            job = multiprocessing.Process(target=process_file_list, args=(chunk, pipeline_config, c))
             job_list.append(job)
 
     # Start all the jobs
@@ -239,6 +224,38 @@ def merge_mfdata(path_to_data: str, prefix='*', overwrite_existing_partials: boo
                                        chunk_size=chunk_size)
 
 
+def process_file_list(file_list, pipeline_config, c):
+    '''Run a PyOPIA processing pipeline for a chuncked list of files based on a given config.toml
+
+    Parameters
+    ----------
+    file_list : str
+        List of file paths to process, where each file will be passed individually through the processing pipeline
+
+    pipeline_config : str
+        Loaded config.toml file to initialize the processing pipeline and setup logging
+
+    c : int
+        Chunk index for tracking progress and logging. If set to 0, enables the
+        progress bar; for other values, the progress bar is disabled.
+    '''
+    processing_pipeline = pyopia.pipeline.Pipeline(pipeline_config)
+    setup_logging(pipeline_config)
+    logger = logging.getLogger('rich')
+
+    with get_custom_progress_bar(f'[blue]Processing progress (chunk {c})', disable=c != 0) as pbar:
+        for filename in pbar.track(file_list, description=f'[blue]Processing progress (chunk {c})'):
+            try:
+                logger.debug(f'Chunk {c} starting to process {filename}')
+                processing_pipeline.run(filename)
+            except Exception as e:
+                logger.warning('[red]An error occured in processing, ' +
+                               'skipping rest of pipeline and moving to next image.' +
+                               f'(chunk {c})')
+                logger.error(e)
+                logger.debug(''.join(traceback.format_tb(e.__traceback__)))
+
+
 def setup_logging(pipeline_config):
     '''Configure logging
 

{pyopia-2.8.0 → pyopia-2.8.2}/pyopia/instrument/silcam.py

@@ -245,7 +245,7 @@ class SilCamLoad():
         self.extension_load = {'.silc': load_rgb8,
                                '.msilc': load_mono8,
                                '.bsilc': load_bayer_rgb8,
-                               '.bmp': skimage.io.imread}
+                               '.bmp': lambda filename: skimage.io.imread(filename).astype(np.float64) / 255}
         self.format_load = {'RGB8': load_rgb8,
                             'MONO8': load_mono8, 'BAYER_RG8': load_bayer_rgb8}
 

pyopia-2.8.0/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '2.8.0'