PyOPIA 2.5.8__tar.gz → 2.5.10__tar.gz

{pyopia-2.5.8 → pyopia-2.5.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOPIA
-Version: 2.5.8
+Version: 2.5.10
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Home-page: https://github.com/sintef/pyopia
 Keywords: Ocean,Particles,Imaging,Measurement,Size distribution

pyopia-2.5.10/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = '2.5.10'

{pyopia-2.5.8 → pyopia-2.5.10}/pyopia/cli.py

@@ -37,7 +37,7 @@ def docs():
 
 @app.command()
 def modify_config(existing_filename: str, modified_filename: str,
-                  raw_files=None,
+                  raw_files=None, pixel_size=None,
                   step_name=None, modify_arg=None, modify_value=None):
     '''Modify a existing config.toml file and write a new one to disc
 
@@ -49,6 +49,8 @@ def modify_config(existing_filename: str, modified_filename: str,
         e.g. config_new.toml
     raw_files : str, optional
         modify the raw file input in the `[general]` settings, by default None
+    pixel_size : str, optional
+        modify the pixel size in the `[general]` settings, by default None
     step_name : str, optional
         the name of the step to modify e.g. `segmentation`, by default None
     modify_arg : str, optional
@@ -61,11 +63,18 @@ def modify_config(existing_filename: str, modified_filename: str,
     toml_settings = pyopia.io.load_toml(existing_filename)
 
     if raw_files is not None:
-        toml_settings['general']['raw_files'] = raw_files
+        toml_settings['general']['raw_files'] = f'{raw_files}'
+    if pixel_size is not None:
+        toml_settings['general']['pixel_size'] = float(pixel_size)
 
     if step_name is not None:
         try:
-            modify_value = float(modify_value)
+            if modify_arg == 'average_window':
+                modify_value = int(modify_value)
+            elif modify_arg == 'threshold':
+                modify_value = float(modify_value)
+            else:
+                modify_value = str(modify_value)
         except ValueError:
             pass
 

{pyopia-2.5.8 → pyopia-2.5.10}/pyopia/io.py

@@ -160,7 +160,11 @@ def load_image_stats(datafilename):
 
 
 def load_stats(datafilename):
-    '''Load STATS file as a DataFrame
+    '''Load -STATS.nc file as xarray Dataset
+
+    .. warning:: Support for loading of old -STATS.h5 formats will be removed in version 3.0.0.
+        They will need to be converted to .nc prior to loading.
+        Data loaded from -STATS.h5 are returned as an xarray Dataset without metadata.
 
     Parameters
     ----------
@@ -169,21 +173,24 @@ def load_stats(datafilename):
 
     Returns
     -------
-    stats : DataFrame
-        STATS DataFrame  / xarray dataset
+    xstats : xarray.Dataset
+        Particle statistics
     '''
 
     if datafilename.endswith('.nc'):
-        with xarray.open_dataset(datafilename) as stats:
-            stats.load()
+        with xarray.open_dataset(datafilename) as xstats:
+            xstats.load()
     elif datafilename.endswith('.h5'):
+        logger.warning('In future, load_stats will only take .nc files')
         stats = pd.read_hdf(datafilename, 'ParticleStats/stats')
+        xstats = stats.to_xarray()
     else:
         logger.warning('WARNING. File extension not specified.' +
                        'Assuming prefix of -STATS.h5 for backwards compatability.' +
-                       'In future, this function will only take .nc files')
+                       'In future, load_stats will only take .nc files')
         stats = pd.read_hdf(datafilename + '-STATS.h5', 'ParticleStats/stats')
-    return stats
+        xstats = stats.to_xarray()
+    return xstats
 
 
 def combine_stats_netcdf_files(path_to_data, prefix='*'):

pyopia-2.5.8/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '2.5.8'