PyOPIA 2.13.0__tar.gz → 2.14.0__tar.gz

{pyopia-2.13.0 → pyopia-2.14.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyOPIA
-Version: 2.13.0
+Version: 2.14.0
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Project-URL: Repository, https://github.com/sintef/pyopia
 Project-URL: Documentation, https://pyopia.readthedocs.io

pyopia-2.14.0/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = "2.14.0"

{pyopia-2.13.0 → pyopia-2.14.0}/pyopia/cf_metadata.json

@@ -62,4 +62,52 @@
     "standard_name": "timestamp",
     "long_name": "Timestamp of particle observation",
     "calculation_method": "Recorded during particle observation",
-    "pyopia_process_level": 0}}
+    "pyopia_process_level": 0},
+"filename": {
+    "standard_name": "filename",
+    "long_name": "Filename of the raw image",
+    "units": "",
+    "calculation_method": "Recorded during image loading",
+    "pyopia_process_level": 0},
+"particle_count": {
+    "standard_name": "particle_count",
+    "long_name": "Number of particles detected in the image",
+    "units": "1",
+    "calculation_method": "Count of particles from segmentation",
+    "pyopia_process_level": 1},
+"saturation": {
+    "standard_name": "image_saturation",
+    "long_name": "Percentage saturation of the image",
+    "units": "percent",
+    "calculation_method": "Computed as the percentage of the image covered by particles relative to the maximum acceptable coverage",
+    "pyopia_process_level": 1},
+"d50": {
+    "standard_name": "median_particle_diameter",
+    "long_name": "Median particle diameter (D50) from volume distribution",
+    "units": "micrometers",
+    "calculation_method": "Calculated from volume-based particle size distribution",
+    "pyopia_process_level": 2},
+"nc": {
+    "standard_name": "number_concentration",
+    "long_name": "Number concentration of particles",
+    "units": "L^-1",
+    "calculation_method": "Calculated from particle count and sample volume",
+    "pyopia_process_level": 2},
+"vc": {
+    "standard_name": "volume_concentration",
+    "long_name": "Volume concentration of particles",
+    "units": "uL L^-1",
+    "calculation_method": "Calculated from particle volumes and sample volume",
+    "pyopia_process_level": 2},
+"sample_volume": {
+    "standard_name": "sample_volume",
+    "long_name": "Volume of water sampled",
+    "units": "L",
+    "calculation_method": "Calculated from image area, pixel size, and path length",
+    "pyopia_process_level": 2},
+"junge": {
+    "standard_name": "junge_parameter",
+    "long_name": "Junge parameter (slope of particle size number distribution)",
+    "units": "1",
+    "calculation_method": "Fitted slope of particle size number distribution between 150-350 µm",
+    "pyopia_process_level": 2}}

{pyopia-2.13.0 → pyopia-2.14.0}/pyopia/exampledata.py

@@ -10,14 +10,18 @@ logger = logging.getLogger()
 
 
 def get_classifier_database_from_pysilcam_blob(download_directory="./"):
-    """Downloads a specified filename from the pysilcam.blob into the working dir. if it doesn't already exist
-
-    only works for known filenames that are on this blob
+    """Downloads and unzips the silcam_database of labelled example images from pysilcam.blob
+    into the working dir. if it doesn't already exist
 
     Parameters
     ----------
-    filename : string
-        known filename on the blob
+    download_directory : string
+        directory to download and unzip the silcam_database.zip into. Defaults to "./"
+
+    Returns
+    -------
+    string
+        download_directory, the directory that the silcam_database.zip was downloaded and unzipped into
 
     """
     if os.path.exists(os.path.join(download_directory)):
@@ -47,6 +51,13 @@ def get_file_from_pysilcam_blob(filename, download_directory="./"):
     ----------
     filename : string
         known filename on the blob
+    download_directory : string
+        directory to download the file into. Defaults to "./"
+
+    Returns
+    -------
+    string
+        filename of the downloaded file
 
     """
     if os.path.exists(os.path.join(download_directory, filename)):
@@ -59,10 +70,16 @@ def get_file_from_pysilcam_blob(filename, download_directory="./"):
 def get_example_silc_image(download_directory="./"):
     """calls `get_file_from_pysilcam_blob` for a silcam iamge
 
+    Parameters
+    ----------
+    download_directory : string
+        directory to download the file into. Defaults to "./"
+
     Returns
     -------
     string
-        filename
+        filename of the downloaded silcam image
+
     """
     filename = "D20181101T142731.838206.silc"
     if os.path.isfile(filename):
@@ -78,6 +95,11 @@ def get_example_model(download_directory="./"):
     Download from the pysilcam blob storage into the working dir.
     If the file exists, skip the download.
 
+    Parameters
+    ----------
+    download_directory : string
+        directory to download the file into. Defaults to "./"
+
     Returns
     -------
     string
@@ -97,6 +119,11 @@ def get_example_model(download_directory="./"):
 def get_example_hologram_and_background(download_directory="./"):
     """calls `get_file_from_pysilcam_blob` for a raw hologram, and its associated background image.
 
+    Parameters
+    ----------
+    download_directory : string
+        directory to download the file into. Defaults to "./"
+
     Returns
     -------
     string

{pyopia-2.13.0 → pyopia-2.14.0}/pyopia/io.py

@@ -128,6 +128,9 @@ def write_stats(
             # Add auxillary data to ximage_stats
             ximage_stats = auxillary_data.add_auxillary_data_to_xstats(ximage_stats)
 
+            # Add CF-compliant attributes
+            ximage_stats = add_cf_attributes(ximage_stats)
+
             encoding_imagestats = setup_xstats_encoding(ximage_stats)
             ximage_stats.to_netcdf(
                 datafilename + "-STATS.nc",

{pyopia-2.13.0 → pyopia-2.14.0}/pyopia/process.py

@@ -639,7 +639,13 @@ class CalculateImageStats():
 
         path_length = getattr(data['settings']['general'], 'path_length', 40)
         if path_length is not None:
-            nc_vc = pyopia.statistics.nc_vc_from_stats(data['stats'], pixel_size, path_length)
+            # Get image dimensions from the corrected image
+            image = data.get('imraw')
+            if image is not None:
+                imy, imx = image.shape[:2]
+            else:
+                imx, imy = 2048, 2448  # fallback defaults
+            nc_vc = pyopia.statistics.nc_vc_from_stats(data['stats'], pixel_size, path_length, imx=imx, imy=imy)
             for k, v in zip(['nc', 'vc', 'sample_volume', 'junge'], nc_vc):
                 data['image_stats'].loc[data['timestamp'], k] = v
 

pyopia-2.13.0/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = "2.13.0"