PyOPIA 2.5.1__tar.gz → 2.5.3__tar.gz

{pyopia-2.5.1 → pyopia-2.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOPIA
-Version: 2.5.1
+Version: 2.5.3
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Home-page: https://github.com/sintef/pyopia
 Keywords: Ocean,Particles,Imaging,Measurement,Size distribution

pyopia-2.5.3/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = '2.5.3'

{pyopia-2.5.1 → pyopia-2.5.3}/pyopia/instrument/holo.py

@@ -681,7 +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-2.5.1 → pyopia-2.5.3}/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-2.5.1 → pyopia-2.5.3}/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-2.5.1 → pyopia-2.5.3}/pyopia/io.py

@@ -213,23 +213,20 @@ def combine_stats_netcdf_files(path_to_data, prefix='*'):
                                coords='minimal', compat='override') as ds:
         xstats = ds.load()
 
-    # Check if we have image statistics in the last file, if so, load it.
-    # The last file should contain the entire time series of processed images.
+    # Check if we have image statistics, if so, load it.
     try:
-        ds = xarray.open_dataset(sorted_filelist[-1], group='image_stats')
+        with xarray.open_mfdataset(sorted_filelist, group='image_stats') as ds:
+            image_stats = ds.load()
     except OSError:
+        logger.info('Could get image_stats from netcdf files for merging, returning None for this.')
         image_stats = None
-    else:
-        image_stats = ds.load()
-    finally:
-        ds.close()
 
     return xstats, image_stats
 
 
 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 +318,6 @@ 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 +372,62 @@ 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-2.5.1 → pyopia-2.5.3}/pyopia/statistics.py

@@ -763,12 +763,14 @@ def make_timeseries_vd(stats, pixel_size, path_length, time_reference):
     similar to Sequoia LISST-100 output,
     and exportable to things like Excel or csv.
 
-    Note: If zero particles are detected within the stats daraframe,
+    Note
+    ----
+    If zero particles are detected within the stats daraframe,
     then the volume concentration should be reported as zero for that
     time. For this function to have awareness of these times, it requires
     time_reference variable. If you use `stats['timestamp'].unique()` for this,
     then you are assuming you have at least one particle per image.
-    It is better to use image_stats['datetime'].values instead, which can be obtained from
+    It is better to use `image_stats['timestamp'].values` instead, which can be obtained from
     :func:`pyopia.io.load_image_stats`
 
     Parameters
@@ -790,9 +792,12 @@ def make_timeseries_vd(stats, pixel_size, path_length, time_reference):
     Example
     -------
     .. code-block:: python
+        path_length = 40  # for a 40mm long path length
+
         time_series_vd = pyopia.statistics.make_timeseries_vd(stats,
                                 settings['general']['pixel_size'],
-                                path_length=40)
+                                path_length,
+                                image_stats['timestamp'].values)
 
         # particle diameters
         dias = np.array(time_series_vd.columns[0:52], dtype=float)
@@ -807,7 +812,7 @@ def make_timeseries_vd(stats, pixel_size, path_length, time_reference):
         time = pd.to_datetime(time_series_vd['Time'].values)
 
         # time-series of total volume concentration
-        vc = np.sum(vdarray, axis=1)
+        volume_concentration = np.sum(vdarray, axis=1)
     '''
     sample_volume = get_sample_volume(pixel_size, path_length=path_length)
 

{pyopia-2.5.1 → pyopia-2.5.3}/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-2.5.1/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '2.5.1'