PyOPIA 2.2.0__tar.gz → 2.3.0__tar.gz

{pyopia-2.2.0 → pyopia-2.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOPIA
-Version: 2.2.0
+Version: 2.3.0
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Home-page: https://github.com/sintef/pyopia
 Keywords: Ocean,Particles,Imaging,Measurement,Size distribution

pyopia-2.3.0/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = '2.3.0'

{pyopia-2.2.0 → pyopia-2.3.0}/pyopia/cli.py

@@ -15,6 +15,7 @@ import pandas as pd
 import pyopia.background
 import pyopia.instrument.silcam
 import pyopia.instrument.holo
+import pyopia.instrument.uvp
 import pyopia.instrument.common
 import pyopia.io
 import pyopia.pipeline
@@ -80,7 +81,7 @@ def generate_config(instrument: str, raw_files: str, model_path: str, outfolder:
     Parameters
     ----------
     instrument : str
-        either `silcam` or `holo`
+        either `silcam`, `holo` or `uvp`
     raw_files : str
         raw_files
     model_path : str
@@ -95,6 +96,8 @@ def generate_config(instrument: str, raw_files: str, model_path: str, outfolder:
             pipeline_config = pyopia.instrument.silcam.generate_config(raw_files, model_path, outfolder, output_prefix)
         case 'holo':
             pipeline_config = pyopia.instrument.holo.generate_config(raw_files, model_path, outfolder, output_prefix)
+        case 'uvp':
+            pipeline_config = pyopia.instrument.uvp.generate_config(raw_files, model_path, outfolder, output_prefix)
 
     config_filename = instrument + "-config.toml"
     with open(config_filename, "w") as toml_file:

{pyopia-2.2.0 → pyopia-2.3.0}/pyopia/instrument/silcam.py

@@ -34,9 +34,9 @@ def load_image(filename):
     Returns
     -------
     array
-        raw image
+        raw image float between 0-1
     '''
-    img = np.load(filename, allow_pickle=False).astype(np.float64)
+    img = np.load(filename, allow_pickle=False).astype(np.float64) / 255
     return img
 
 
@@ -68,7 +68,7 @@ class SilCamLoad():
 
     def __call__(self, data):
         timestamp = timestamp_from_filename(data['filename'])
-        img = load_image(data['filename']).astype(np.float64)/255
+        img = load_image(data['filename'])
         data['timestamp'] = timestamp
         data['imraw'] = img
         return data

pyopia-2.3.0/pyopia/instrument/uvp.py

@@ -0,0 +1,127 @@
+'''
+Module containing UVP specific tools to enable compatability with the :mod:`pyopia.pipeline`
+'''
+
+import os
+import numpy as np
+import pandas as pd
+import skimage.io
+
+
+def timestamp_from_filename(filename):
+    '''get a pandas timestamp from a UVP vignette image filename
+
+    Args:
+        filename (string): UVP filename (.png)
+
+    Returns:
+        timestamp: timestamp from pandas.to_datetime()
+    '''
+
+    # get the timestamp of the image (in this case from the filename)
+    timestr = os.path.split(filename)[-1].strip('.png')
+    timestamp = pd.to_datetime(timestr)
+    return timestamp
+
+
+def load_image(filename):
+    '''load a UVP .png file from disc
+
+    Parameters
+    ----------
+    filename : string
+        filename to load
+
+    Returns
+    -------
+    array
+        raw image float between 0-1, inverted so that particles are dark on a light background
+    '''
+    img_darkfield = skimage.io.imread(filename).astype(np.float64)
+    img_inverted = (255 - img_darkfield) / 255
+    return img_inverted
+
+
+class UVPLoad():
+    '''PyOpia pipline-compatible class for loading a single UVP image
+    using :func:`pyopia.instrument.uvp.load_image`
+    and extracting the timestamp using
+    :func:`pyopia.instrument.uvp.timestamp_from_filename`
+
+    Pipeline input data:
+    ---------
+    :class:`pyopia.pipeline.Data`
+        containing the following keys:
+
+        :attr:`pyopia.pipeline.Data.filename`
+
+    Returns:
+    --------
+    :class:`pyopia.pipeline.Data`
+        containing the following new keys:
+
+        :attr:`pyopia.pipeline.Data.timestamp`
+
+        :attr:`pyopia.pipeline.Data.img`
+    '''
+
+    def __init__(self):
+        pass
+
+    def __call__(self, data):
+        timestamp = timestamp_from_filename(data['filename'])
+        img = load_image(data['filename'])
+        data['timestamp'] = timestamp
+        data['imraw'] = img
+        return data
+
+
+def generate_config(raw_files: str, model_path: str, outfolder: str, output_prefix: str):
+    '''Generate example uvp config.toml as a dict
+
+    Parameters
+    ----------
+    raw_files : str
+        raw_files
+    model_path : str
+        model_path
+    outfolder : str
+        outfolder
+    output_prefix : str
+        output_prefix
+
+    Returns:
+    --------
+    dict
+        pipeline_config toml dict
+    '''
+    # define the configuration to use in the processing pipeline - given as a dictionary - with some values defined above
+    pipeline_config = {
+        'general': {
+            'raw_files': raw_files,
+            'pixel_size': 80  # pixel size in um
+        },
+        'steps': {
+            'classifier': {
+                'pipeline_class': 'pyopia.classify.Classify',
+                'model_path': model_path
+            },
+            'load': {
+                'pipeline_class': 'pyopia.instrument.uvp.UVPLoad'
+            },
+            'segmentation': {
+                'pipeline_class': 'pyopia.process.Segment',
+                'threshold': 0.95,
+                'segment_source': 'imraw'
+            },
+            'statextract': {
+                'pipeline_class': 'pyopia.process.CalculateStats',
+                'roi_source': 'imraw'
+            },
+            'output': {
+                'pipeline_class': 'pyopia.io.StatsH5',
+                'output_datafile': os.path.join(outfolder, output_prefix)
+            }
+        }
+    }
+    return pipeline_config

pyopia-2.2.0/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '2.2.0'