PyOPIA 1.1.2__tar.gz → 1.1.4__tar.gz

{pyopia-1.1.2 → pyopia-1.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyOPIA
-Version: 1.1.2
+Version: 1.1.4
 Summary: A Python Ocean Particle Image Analysis toolbox.
 Home-page: https://github.com/sintef/pyopia
 Keywords: Ocean,Particles,Imaging,Measurement,Size distribution

pyopia-1.1.4/pyopia/__init__.py

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

{pyopia-1.1.2 → pyopia-1.1.4}/pyopia/pipeline.py

@@ -69,19 +69,11 @@ class Pipeline():
         self.data['settings'] = settings
 
         self.pass_general_settings()
-        print('raw_files:', self.data['raw_files'])
 
         for stepname in self.stepnames:
             if not self.initial_steps.__contains__(stepname):
                 continue
-            if stepname == 'classifier':
-                callobj = self.step_callobj(stepname)
-                self.data['cl'] = callobj()
-            else:
-                callobj = self.step_callobj(stepname)
-                self.data = callobj(self.data)
-
-        print('Pipeline ready with these data: ', list(self.data.keys()))
+            self.run_step(stepname)
 
     def run(self, filename):
         '''Method for executing the processing pipeline.
@@ -109,14 +101,40 @@ class Pipeline():
             if self.initial_steps.__contains__(stepname):
                 continue
 
-            callobj = self.step_callobj(stepname)
-            self.data = callobj(self.data)
+            self.run_step(stepname)
 
         stats = self.data['stats']
 
         return stats
 
+    def run_step(self, stepname):
+        '''Execute a pipeline step and update the pipeline data
+
+        Parameters
+        ----------
+        stepname : str
+            Name of the step defined in the settings
+        '''
+        if stepname == 'classifier':
+            callobj = self.step_callobj(stepname)
+            self.data['cl'] = callobj()
+        else:
+            callobj = self.step_callobj(stepname)
+            self.data = callobj(self.data)
+
     def step_callobj(self, stepname):
+        '''Generate a callable object for use in run_step()
+
+        Parameters
+        ----------
+        stepname : str
+            Name of the step defined in the settings
+
+        Returns
+        -------
+        obj
+            callable object for use in run_step()
+        '''
 
         pipeline_class = self.settings['steps'][stepname]['pipeline_class']
         classname = pipeline_class.split('.')[-1]
@@ -254,7 +272,7 @@ class ReturnData():
     .. code-block:: python
 
         [steps.returndata]
-        pipeline_class = 'pyopia.classify.ReturnData'
+        pipeline_class = 'pyopia.pipeline.ReturnData'
 
     This will allow you to call pipeline.run() like this:
 

{pyopia-1.1.2 → pyopia-1.1.4}/pyopia/process.py

@@ -427,9 +427,10 @@ def statextract(imbw, timestamp, imc,
     if not len(s) == 3:
         imref = np.copy(imc)
         imc = np.zeros((np.shape(imc)[0], np.shape(imc)[1], 3), dtype=np.uint8)
-        imc[:, :, 0] = imref
-        imc[:, :, 1] = imref
-        imc[:, :, 2] = imref
+        # 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!')
 
     stats = extract_particles(imc, timestamp, Classification, region_properties,

pyopia-1.1.2/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '1.1.2'