PyOPIA 2.5.0__tar.gz → 2.5.2__tar.gz

{pyopia-2.5.0 → pyopia-2.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOPIA
-Version: 2.5.0
+Version: 2.5.2
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Home-page: https://github.com/sintef/pyopia
 Keywords: Ocean,Particles,Imaging,Measurement,Size distribution

pyopia-2.5.2/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = '2.5.2'

{pyopia-2.5.0 → pyopia-2.5.2}/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
@@ -680,7 +681,7 @@ def generate_config(raw_files: str, model_path: str, outfolder: str, output_pref
                 'pipeline_class': 'pyopia.instrument.holo.MergeStats',
             },
             'output': {
-                'pipeline_class': 'pyopia.io.StatsH5',
+                'pipeline_class': 'pyopia.io.StatsToDisc',
                 'output_datafile': os.path.join(outfolder, output_prefix)
             }
         }

{pyopia-2.5.0 → pyopia-2.5.2}/pyopia/instrument/silcam.py

@@ -1,5 +1,10 @@
 '''
 Module containing SilCam specific tools to enable compatability with the :mod:`pyopia.pipeline`
+
+See:
+Davies, E. J., Brandvik, P. J., Leirvik, F., & Nepstad, R. (2017). The use of wide-band transmittance imaging to size and
+classify suspended particulate matter in seawater. Marine Pollution Bulletin,
+115(1–2). https://doi.org/10.1016/j.marpolbul.2016.11.063
 '''
 
 import os
@@ -14,11 +19,12 @@ def timestamp_from_filename(filename):
 
     Parameters
     ----------
-        filename (string): silcam filename (.silc)
+    filename (string): silcam filename (.silc)
 
     Returns
     -------
-        timestamp: timestamp from pandas.to_datetime()
+    timestamp: timestamp
+        timestamp from pandas.to_datetime()
     '''
 
     # get the timestamp of the image (in this case from the filename)
@@ -332,7 +338,7 @@ def generate_config(raw_files: str, model_path: str, outfolder: str, output_pref
                 'roi_source': 'imref'
             },
             'output': {
-                'pipeline_class': 'pyopia.io.StatsH5',
+                'pipeline_class': 'pyopia.io.StatsToDisc',
                 'output_datafile': os.path.join(outfolder, output_prefix)
             }
         }

{pyopia-2.5.0 → pyopia-2.5.2}/pyopia/instrument/uvp.py

@@ -117,7 +117,7 @@ def generate_config(raw_files: str, model_path: str, outfolder: str, output_pref
                 'roi_source': 'imraw'
             },
             'output': {
-                'pipeline_class': 'pyopia.io.StatsH5',
+                'pipeline_class': 'pyopia.io.StatsToDisc',
                 'output_datafile': os.path.join(outfolder, output_prefix)
             }
         }

{pyopia-2.5.0 → pyopia-2.5.2}/pyopia/io.py

@@ -229,7 +229,7 @@ def combine_stats_netcdf_files(path_to_data, prefix='*'):
 
 def merge_and_save_mfdataset(path_to_data, prefix='*'):
     '''Combine a multi-file directory of STATS.nc files into a single '-STATS.nc' file
-    that can then be loaded with {func}`pyopia.io.load_stats`
+    that can then be loaded with :func:`pyopia.io.load_stats`
 
     Parameters
     ----------
@@ -321,8 +321,6 @@ def show_h5_meta(h5file):
 class StatsToDisc():
     '''PyOpia pipline-compatible class for calling write_stats() that created NetCDF files.
 
-    Replaces the old StatsH5 class
-
     Parameters
     ----------
     output_datafile : str
@@ -377,10 +375,62 @@ class StatsToDisc():
         return data
 
 
-StatsH5 = StatsToDisc
+def load_toml(toml_file):
+    '''Load a TOML settings file from file
 
+    Parameters
+    ----------
+    toml_file : str
+        TOML filename
 
-def load_toml(toml_file):
+    Returns
+    -------
+    settings : dict
+        TOML settings
+    '''
     with open(toml_file, 'r') as f:
         settings = toml.load(f)
     return settings
+
+
+def StatsH5():
+    '''.. deprecated:: 2.4.8
+        :class:`pyopia.io.StatsH5` will be removed in version 3.0.0, it is replaced by
+        :class:`pyopia.io.StatsToDisc`.
+
+    PyOpia pipline-compatible class for calling write_stats() that creates h5 files.
+
+    Parameters
+    ----------
+    output_datafile : str
+        prefix path for output nc file
+    dataformat : str
+        either 'nc' or 'h5
+    export_name_len : int
+        max number of chars allowed for col 'export name'. Defaults to 40
+    append : bool
+        Append all processed data into one nc file.
+        Defaults to True.
+        If False, then one nc file will be generated per raw image,
+        which can be loaded using :func:`pyopia.io.combine_stats_netcdf_files`
+        This is useful for larger datasets, where appending causes substantial slowdown
+        as the dataset gets larger.
+
+    Returns
+    -------
+    data : :class:`pyopia.pipeline.Data`
+        data from the pipeline
+
+    Example
+    -------
+    Example config for pipeline useage:
+
+    .. code-block:: toml
+
+        [steps.output]
+        pipeline_class = 'pyopia.io.StatsH5'
+        output_datafile = './test' # prefix path for output nc file
+        append = true
+    '''
+    logger.warning('StatsH5 will be removed in version 3.0.0, it is replaced by pyopia.io.StatsToDisc')
+    return StatsToDisc()

{pyopia-2.5.0 → pyopia-2.5.2}/pyopia/tests/test_pipeline.py

@@ -93,7 +93,7 @@ def test_holo_pipeline():
                     'pipeline_class': 'pyopia.instrument.holo.MergeStats',
                 },
                 'output': {
-                    'pipeline_class': 'pyopia.io.StatsH5',
+                    'pipeline_class': 'pyopia.io.StatsToDisc',
                     'output_datafile': datafile_prefix
                 }
             }
@@ -164,7 +164,7 @@ def test_silcam_pipeline():
                     'roi_source': 'im_minimum'
                 },
                 'output': {
-                    'pipeline_class': 'pyopia.io.StatsH5',
+                    'pipeline_class': 'pyopia.io.StatsToDisc',
                     'output_datafile': datafile_prefix
                 }
             }

pyopia-2.5.0/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '2.5.0'