PyOPIA 1.1.4__tar.gz → 1.1.6__tar.gz

{pyopia-1.1.4 → pyopia-1.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOPIA
-Version: 1.1.4
+Version: 1.1.6
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Home-page: https://github.com/sintef/pyopia
 Keywords: Ocean,Particles,Imaging,Measurement,Size distribution
@@ -60,18 +60,6 @@ A Python Ocean Particle Image Analysis toolbox
 
 - Under development. See/regester issues, [here](https://github.com/SINTEF/pyopia/issues)
 
-----
-
-# Installing for users
-
-Users are expected to be familiar with Python, and have [Python](https://github.com/conda-forge/miniforge/#download), [pip](https://pypi.org/project/pip/). You can then install Pyopia like this:
-
-```
-pip install pyopia
-```
-
-We would usually recommend installing within a virtual python environment, which you can read more about [here](https://jni.github.io/using-python-for-science/intro-to-environments.html).
-
 ----
 # Development targets for PyOpia:
 
@@ -101,9 +89,15 @@ We welcome additions and improvements to the code! We request that you follow a
 4. All pull requests must be reviewed by a person. The benefits from code review are plenty, but we like to emphasise that code reviews help spreading the awarenes of code changes. Please note that code reviews should be a pleasant experience, so be plesant, polite and remember that there is a human being with good intentions on the other side of the screen.
 5. All contributions are linted with flake8. We recommend that you run flake8 on your code while developing to fix any issues as you go. We recommend using autopep8 to autoformat your Python code (but please check the code behaviour is not affected by autoformatting before pushing). This makes flake8 happy, and makes it easier for us all to maintain a consistent and readable code base.
 
-## Installing from source for developers
+# Installing
+
+## For users
+
+Users are expected to be familiar with Python. Please refer to the recommended installation instructions provided on the documentation pages, [here](https://pyopia.readthedocs.io/en/latest/intro.html#installing)
 
-Install [Python](https://github.com/conda-forge/miniforge/#download).
+## For developers from source
+
+Install [Python](https://github.com/conda-forge/miniforge/#download) version 3.10.
 
 A prompt such as is provided by the [miniforge installation](https://github.com/conda-forge/miniforge/#download) may be used for the following:
 
@@ -142,6 +136,18 @@ conda activate pyopia
 poetry install
 ```
 
+Optional dependecies (for classification), can be installed like this:
+
+```bash
+poetry install --extras "classification"
+```
+
+or for arm/silicon systems:
+
+```bash
+poetry install --extras "classification-arm64"
+```
+
 3. (optional) Run local tests:
 
 ```bash

{pyopia-1.1.4 → pyopia-1.1.6}/README.md

@@ -12,18 +12,6 @@ A Python Ocean Particle Image Analysis toolbox
 
 - Under development. See/regester issues, [here](https://github.com/SINTEF/pyopia/issues)
 
-----
-
-# Installing for users
-
-Users are expected to be familiar with Python, and have [Python](https://github.com/conda-forge/miniforge/#download), [pip](https://pypi.org/project/pip/). You can then install Pyopia like this:
-
-```
-pip install pyopia
-```
-
-We would usually recommend installing within a virtual python environment, which you can read more about [here](https://jni.github.io/using-python-for-science/intro-to-environments.html).
-
 ----
 # Development targets for PyOpia:
 
@@ -53,9 +41,15 @@ We welcome additions and improvements to the code! We request that you follow a
 4. All pull requests must be reviewed by a person. The benefits from code review are plenty, but we like to emphasise that code reviews help spreading the awarenes of code changes. Please note that code reviews should be a pleasant experience, so be plesant, polite and remember that there is a human being with good intentions on the other side of the screen.
 5. All contributions are linted with flake8. We recommend that you run flake8 on your code while developing to fix any issues as you go. We recommend using autopep8 to autoformat your Python code (but please check the code behaviour is not affected by autoformatting before pushing). This makes flake8 happy, and makes it easier for us all to maintain a consistent and readable code base.
 
-## Installing from source for developers
+# Installing
+
+## For users
+
+Users are expected to be familiar with Python. Please refer to the recommended installation instructions provided on the documentation pages, [here](https://pyopia.readthedocs.io/en/latest/intro.html#installing)
 
-Install [Python](https://github.com/conda-forge/miniforge/#download).
+## For developers from source
+
+Install [Python](https://github.com/conda-forge/miniforge/#download) version 3.10.
 
 A prompt such as is provided by the [miniforge installation](https://github.com/conda-forge/miniforge/#download) may be used for the following:
 
@@ -94,6 +88,18 @@ conda activate pyopia
 poetry install
 ```
 
+Optional dependecies (for classification), can be installed like this:
+
+```bash
+poetry install --extras "classification"
+```
+
+or for arm/silicon systems:
+
+```bash
+poetry install --extras "classification-arm64"
+```
+
 3. (optional) Run local tests:
 
 ```bash

pyopia-1.1.6/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = '1.1.6'

{pyopia-1.1.4 → pyopia-1.1.6}/pyopia/background.py

@@ -94,12 +94,7 @@ def correct_im_accurate(imbg, imraw):
     '''
 
     imc = np.float64(imraw) - np.float64(imbg)
-    if imc.ndim == 3:
-        imc[:, :, 0] += (255 / 2 - np.percentile(imc[:, :, 0], 50))
-        imc[:, :, 1] += (255 / 2 - np.percentile(imc[:, :, 1], 50))
-        imc[:, :, 2] += (255 / 2 - np.percentile(imc[:, :, 2], 50))
-    else:
-        imc += (255 / 2 - np.percentile(imc, 50))
+    imc += (255 / 2 - np.percentile(imc, 50))
 
     imc += 255 - imc.max()
 

{pyopia-1.1.4 → pyopia-1.1.6}/pyopia/instrument/holo.py

@@ -242,7 +242,7 @@ def create_kernel(im, pixel_size, wavelength, n, offset, minZ, maxZ, stepZ):
 
     f = (np.pi / (pixel_size / 1e6)) * (f1**2 + f2**2)**0.5
 
-    z = (np.arange(minZ * 1e-3, maxZ * 1e-3, stepZ * 1e-3) / n) + (offset * 1e-3)
+    z = (np.arange(minZ * 1e-3, (maxZ + stepZ) * 1e-3, stepZ * 1e-3) / n) + (offset * 1e-3)
 
     wavelength_m = wavelength * 1e-9
     k = 2 * np.pi / wavelength_m

{pyopia-1.1.4 → pyopia-1.1.6}/pyopia/instrument/silcam.py

@@ -3,9 +3,9 @@ Module containing SilCam specific tools to enable compatability with the :mod:`p
 '''
 
 import os
-
 import numpy as np
 import pandas as pd
+from skimage.exposure import rescale_intensity
 
 
 def timestamp_from_filename(filename):
@@ -36,7 +36,7 @@ def load_image(filename):
     array
         raw image
     '''
-    img = np.load(filename, allow_pickle=False).astype(np.float64)
+    img = np.load(filename, allow_pickle=False).astype(np.uint8)
     return img
 
 
@@ -97,9 +97,11 @@ class ImagePrep():
 
     def __call__(self, data):
         image = data[self.image_level]
-        data['imref'] = image
         imc = np.float64(image)
 
+        image = rescale_intensity(image, out_range=(0, 255))
+        data['imref'] = np.uint8(image)
+
         # simplify processing by squeezing the image dimensions into a 2D array
         # min is used for squeezing to represent the highest attenuation of all wavelengths
         imc = np.min(imc, axis=2)

{pyopia-1.1.4 → pyopia-1.1.6}/pyopia/process.py

@@ -286,7 +286,7 @@ def extract_particles(imc, timestamp, Classification, region_properties,
 
             if Classification is not None:
                 # run a prediction on what type of particle this might be
-                prediction = Classification.proc_predict(roi.astype(np.uint8))
+                prediction = Classification.proc_predict(roi)
                 predictions[int(i), :] = prediction[0]
 
             # add the roi to the HDF5 file
@@ -336,8 +336,7 @@ def measure_particles(imbw, max_particles=5000):
 
     # if there are too many particles then do no proceed with analysis
     if (iml.max() > max_particles):
-        print('....that''s way too many particles! Skipping image.')
-        imbw *= 0  # this is not a good way to handle this condition
+        raise RuntimeError('Too many particles. Refer to documentation on max_particles parameter in measure_particles()')
         # @todo handle situation when too many particles are found
 
     region_properties = measure.regionprops(iml, cache=False)
@@ -424,14 +423,14 @@ def statextract(imbw, timestamp, imc,
 
     # build the stats and export to HDF5
     s = np.shape(imc)
-    if not len(s) == 3:
+    if len(s) == 2:
         imref = np.copy(imc)
         imc = np.zeros((np.shape(imc)[0], np.shape(imc)[1], 3), dtype=np.uint8)
         # Convert from floats in [0, 1] to ints in [0, 255]
         imc[:, :, 0] = 255 * imref
         imc[:, :, 1] = 255 * imref
         imc[:, :, 2] = 255 * imref
-        print('WARNING. exportparticles temporarily modified for 2-d images without color!')
+        print('WARNING! Unexpected image dimension. extract_particles modified for 2-d images without color!')
 
     stats = extract_particles(imc, timestamp, Classification, region_properties,
                               export_outputpath=export_outputpath, min_length=min_length,
@@ -537,7 +536,13 @@ class CalculateStats():
 
     def __call__(self, data):
         print('statextract')
-        stats, saturation = statextract(data['imbw'], data['timestamp'], data['imc'],
+        if 'imref' not in data.keys():
+            if data['cl'] is not None:
+                print('WARNING. No reference image ("imref") for classifier. Resorting to "imc"')
+            imc = data['imc']
+        else:
+            imc = data['imref']
+        stats, saturation = statextract(data['imbw'], data['timestamp'], imc,
                                         Classification=data['cl'],
                                         max_coverage=self.max_coverage,
                                         max_particles=self.max_particles,

{pyopia-1.1.4 → pyopia-1.1.6}/pyopia/statistics.py

@@ -296,13 +296,14 @@ def vd_from_stats(stats, pix_size):
     return dias, vd
 
 
-def make_montage(stats_file, pixel_size, roidir,
+def make_montage(stats_file_or_df, pixel_size, roidir,
                  auto_scaler=500, msize=1024, maxlength=100000, crop_stats=None, brightness=255, eyecandy=True):
     '''
     makes nice looking montage from a directory of extracted particle images
 
     Args:
-        stats_file                  : location of the stats hdf5 or nc file that comes from processing
+        stats_file_or_df           : either a str specifying the location of the STATS.nc file that comes from processing,
+                                      or a stats dataframe
         pixel_size                  : pixel size of system defined by settings.PostProcess.pix_size
         roidir                      : location of roifiles usually defined by settings.ExportParticles.outputpath
         auto_scaler=500             : approximate number of particle that are attempted to be packed into montage
@@ -318,7 +319,10 @@ def make_montage(stats_file, pixel_size, roidir,
                                       which can be plotted using plotting.montage_plot(montage, settings.PostProcess.pix_size)
     '''
 
-    stats = load_stats_as_dataframe(stats_file)
+    if isinstance(stats_file_or_df, str):
+        stats = load_stats_as_dataframe(stats_file_or_df)
+    else:
+        stats = stats_file_or_df
 
     if crop_stats is not None:
         stats = crop_stats(stats, crop_stats)

pyopia-1.1.4/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '1.1.4'