Merge pull request #28 from TomSlater/version_030

Version 0.3.0 Update

Author: TomSlater

ParticleSpy/ParticleAnalysis.py

@@ -51,13 +51,15 @@ def ParticleAnalysis(acquisition,parameters,particles=None,mask=np.zeros((1))):
 
     if mask == 'UI':
         labeled = label(np.load(inspect.getfile(process).rpartition('\\')[0]+'/Parameters/manual_mask.npy'))
+        plt.imshow(labeled)
+        #morphology.remove_small_objects(labeled,30,in_place=True)
     elif mask.sum()==0:
         labeled = process(image,parameters)
         #labels = np.unique(labeled).tolist() #some labeled number have been removed by "remove_small_holes" function
     else:
         labeled = label(mask)
 
-    for region in regionprops(labeled): #'count' start with 1, 0 is background
+    for region in regionprops(labeled, coordinates='rc'): #'count' start with 1, 0 is background
         p = Particle()
 
         p_im = np.zeros_like(image.data)
@@ -97,7 +99,7 @@ def ParticleAnalysis(acquisition,parameters,particles=None,mask=np.zeros((1))):
         p.set_eccentricity(eccentricity)
 
         #Set total image intensity
-        intensity = (image.data*maskp).sum() - p.background
+        intensity = ((image.data - p.background)*maskp).sum()
         p.set_intensity(intensity)
 
         #Set zoneaxis
@@ -118,7 +120,7 @@ def ParticleAnalysis(acquisition,parameters,particles=None,mask=np.zeros((1))):
 
         if isinstance(acquisition,list):
             p.spectrum = {}
-            for ac in acquisition:
+            for ac in acquisition[1:]:
                 if ac.metadata.Signal.signal_type == 'EDS_TEM':
                     ac.set_elements(parameters.eds['elements'])
                     ac.add_lines()
@@ -128,7 +130,6 @@ def ParticleAnalysis(acquisition,parameters,particles=None,mask=np.zeros((1))):
                     if parameters.eds["factors"]!=False:
                         get_composition(p,parameters)
                 elif ac.metadata.Signal.signal_type == 'EELS':
-                    ac.add_elements(parameters.eds['elements'])
                     if 'high-loss' in ac.metadata.General.title:
                         store_spectrum(p,ac,'EELS-HL')
                     elif 'low-loss' in ac.metadata.General.title:

ParticleSpy/SegUI.py

@@ -248,12 +248,12 @@ def update(self):
         self.label.setPixmap(pixmap2)
 
         self.prev_params.load()
-        self.prev_params.save(filename=inspect.getfile(process).rpartition('\\')[0]+'/Parameters/parameters_previous.hdf5')
+        self.prev_params.save(filename=inspect.getfile(process).rpartition('\\')[0]+'/parameters/parameters_previous.hdf5')
 
         self.params.save()
 
     def undo(self):
-        self.params.load(filename='Parameters/parameters_previous.hdf5')
+        self.params.load(filename='parameters/parameters_previous.hdf5')
 
         labels = process(self.im_hs,self.params)
         labels = np.uint8(labels*(256/labels.max()))
@@ -325,7 +325,7 @@ def mousePressEvent(self, e):
             pixmap = QPixmap(qi)
 
             painter = QPainter(self.pixmap())
-            painter.setOpacity(0.01)
+            painter.setOpacity(0.1)
 
             painter.drawPixmap(0, 0, pixmap)
             painter.end()
@@ -358,8 +358,8 @@ def mouseReleaseEvent(self, e):
         self.last_y = None
 
     def savearray(self,image):
-        resized = np.array(Image.fromarray(self.array).resize((image.shape[0],image.shape[1])))
-        np.save(inspect.getfile(process).rpartition('\\')[0]+'/Parameters/manual_mask',resized)
+        resized = np.array(Image.fromarray(self.array).resize((image.shape[1],image.shape[0])))
+        np.save(inspect.getfile(process).rpartition('\\')[0]+'/parameters/manual_mask',resized)
 
 
 def main(haadf):

setup.py

@@ -18,7 +18,7 @@
 setuptools.setup(
     name="particlespy",
     package_dir={'particlespy':'particlespy'},
-    version="0.2.0",
+    version="0.3.0",
     author="Thomas Slater",
     author_email="tjaslater@gmail.com",
     description="A package to perform particle segmentation and analysis",
@@ -31,8 +31,8 @@
     package_data={
         'ParticleSpy':
         [
-            'Data/*.dm4',
-            'Parameters/*.hdf5'
+            'data/*.dm4',
+            'parameters/*.hdf5'
         ],
     },
     classifiers=[