PYME-extra 1.0.4.post0__py3-none-any.whl

PYMEcs/experimental/procPoints.py

@@ -0,0 +1,77 @@
+from PYME.IO.MetaDataHandler import NestedClassMDHandler
+from PYME.IO.image import ImageStack
+from PYME.DSView import ViewIm3D
+import numpy as np
+import wx
+from PYMEcs.misc.guiMsgBoxes import Warn
+from scipy.ndimage import gaussian_filter
+
+from traits.api import HasTraits, Str, Int, CStr, List, Enum, Float
+#from traitsui.api import View, Item, Group
+#from traitsui.menu import OKButton, CancelButton, OKCancelButtons
+
+class procPtsChoice(HasTraits):
+    minimal_distance_in_nm = Float(30)
+    sigma_for_Gaussian_blur = Float(2)
+
+
+class procPts:
+    """
+GUI class to process point positions produced by blobfind 
+    """
+    def __init__(self, dsviewer):
+        self.dsviewer = dsviewer
+        self.procPtsSel = procPtsChoice()
+
+        dsviewer.AddMenuItem('Experimental>Object Processing',
+                             'Set all pixels of detected object centers in new image',
+                             self.OnProcPoints)
+
+    def OnProcPoints(self, event=None):
+        try:
+            points = self.dsviewer.view.points
+        except AttributeError:
+            Warn(None, 'no object locations found')
+            return
+
+        if len(self.dsviewer.view.points) < 1:
+            Warn(None, 'object location list empty')
+            return
+        
+        if not self.procPtsSel.configure_traits(kind='modal'):
+            return
+        
+        xp = np.rint(self.dsviewer.view.points[:,0])
+        yp = np.rint(self.dsviewer.view.points[:,1])
+
+        mindistnm = self.procPtsSel.minimal_distance_in_nm # make this an option
+        mindistpix = mindistnm / (1e3*self.dsviewer.image.mdh.voxelsize.x)
+        # here we need some code to remove points with NND < mindist
+        xd = np.subtract.outer(xp,xp)
+        yd = np.subtract.outer(yp,yp)
+        d = np.sqrt(xd**2+yd**2)
+        np.fill_diagonal(d,1e6)
+        dmin = d.min(0)
+        xp2 = xp[dmin >= mindistpix]
+        yp2 = yp[dmin >= mindistpix]
+        
+        imd = np.zeros(self.dsviewer.image.data.shape[0:2])
+        imd[xp2.astype('i'),yp2.astype('i')] = 1
+        sigma = self.procPtsSel.sigma_for_Gaussian_blur # in future may make this a config parameter
+        imf = gaussian_filter(imd,sigma)
+        
+        im = ImageStack(imf, titleStub = 'object positions')
+        mdh2 = NestedClassMDHandler(self.dsviewer.image.mdh)
+        im.mdh.copyEntriesFrom(mdh2)
+
+        if self.dsviewer.mode == 'visGUI':
+            mode = 'visGUI'
+        else:
+            mode = 'lite'
+
+        dv = ViewIm3D(im, mode=mode, glCanvas=self.dsviewer.glCanvas,
+                      parent=wx.GetTopLevelParent(self.dsviewer))
+
+
+def Plug(dsviewer):
+    procPts(dsviewer)

PYMEcs/experimental/pyme2caml.py

@@ -0,0 +1,73 @@
+import wx
+import numpy as np
+
+def pipelineSaveCSV(pipeline,filename,keys):
+    pipeline.save_txt(filename,keys)
+
+
+def p_fileinfo(pipeline,keys):
+    xlim = [float(pipeline['x'].min()),float(pipeline['x'].max())]
+    ylim = [float(pipeline['y'].min()),float(pipeline['y'].max())]
+    fileinfo = dict(xCol = keys.index('x'),
+                    yCol= keys.index('y'),
+                    ChanIDCol= None,
+                    ClusMembershipIDCol = None,
+                    LabelIDCol = None,
+                    UIDCol = None)
+    fileinfo.update(dict(InputFileDelimiter=',',InputFileExt='.csv'))
+    fileinfo.update(dict(AutoAxes=False,
+                         AutoAxesNearest=1000,
+                         ImageSize=[xlim[1]-xlim[0],ylim[1]-ylim[0],0],
+                         DataScale=1,
+                         xMin=xlim[0],
+                         xMax=xlim[1],
+                         yMin=ylim[0],
+                         yMax=ylim[1]))
+    fileinfo.update(dict(ClosestFriend=1,
+                         FurthestFriend=100))
+    return fileinfo
+
+
+def pipelineSaveJSON(pipeline,filename,keys):
+    import json
+    fileinfo = p_fileinfo(pipeline,keys)
+    
+    with open(filename,"w+") as file:
+        json.dump(fileinfo, file,skipkeys=True,indent=3)
+
+
+class IOcaml:
+    """
+
+    """
+    def __init__(self, visFr):
+        self.visFr = visFr
+        self.pipeline = visFr.pipeline
+
+        visFr.AddMenuItem('Experimental>Deprecated>IO', "Save event data to CSV and JSON for CAML",self.OnSaveCaml)
+
+    def OnSaveCaml(self,event):
+        import os
+        pipeline = self.pipeline
+        keys = ['x','y','t','A','error_x','error_y']
+        if 'sig' in pipeline.keys():
+            keys.append('sig')
+        if 'dbscanClumpID' in pipeline.keys():
+            keys.append('dbscanClumpID')
+        if 'nPhotons' in pipeline.keys():
+            keys.append('nPhotons')
+        if 'nchi2' in pipeline.keys():
+            keys.append('nchi2')
+        
+        filename = wx.FileSelector('Save events for CAML (select basename)...',
+                                   wildcard="CSV files (*.csv)|*.csv", 
+                                   flags = wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
+                                   
+        if not filename == '':
+            base, ext = os.path.splitext(filename)
+            pipelineSaveCSV(pipeline,base+".csv",keys)
+            pipelineSaveJSON(pipeline,base+".json",keys)
+
+def Plug(visFr):
+    """Plugs this module into the gui"""
+    visFr.iocaml = IOcaml(visFr)