icy integration

applications/clem_icy.py

@@ -11,8 +11,8 @@ import xml.etree.ElementTree as ET
 
 import sys
 import os
-
-
+import glob
+import numpy as np
 
 
 
@@ -122,6 +122,108 @@ for regpt in em_regpts:
 pts2xml(mm_fm['mapfile'], fm_px)
 pts2xml(mm_em['mergefile'], em_px)
 
+
+##                ICY   runs here      
+
+
+print('----------------------------------------------------------------')
+print('        Starting Icy..................................')
+print('----------------------------------------------------------------')
+print(' Please run ec-CLEM and when done click SHOW ROIs ON ORIGINAL SOURCE IMAGE\n')
+
+
+workdir = os.getcwd()
+
+os.chdir('C:\Software\icy')
+icycmd = 'java -jar icy.jar -x plugins.tprovoost.scripteditor.main.ScriptEditorPlugin C:\Software\opener.js'
+
+os.system(icycmd +' '+ mm_fm['mapfile'] +' '+  mm_em['mergefile'] + os.path.splitext(mm_em['mapfile'])[1])
+
+os.chdir(workdir)
+
+
+#%%
+
+# import icy XMLs
+
+x_emf = mm_em['mergefile']+ os.path.splitext( mm_em['mapfile'])[1] + '_ROIsavedwhenshowonoriginaldata' + '.xml'
+x_trafo = mm_fm['mapfile'] + '_transfo' + '.xml'
+
+if not all([os.path.exists(x_emf),os.path.exists(x_trafo)]):  raise ValueError('Could not find the results of Icy registration. Please re-run.')
+    
+root_em = ET.parse(x_emf)
+root_trafo = ET.parse(x_trafo)
+
+
+# extract transformation matrices
+
+mat = []
+if root_trafo.find('MatrixTransformation') == None:
+    root_trafo = ET.parse(glob.glob(mm_fm['mapfile'] + '_transfo' + '*back-up.xml')[-1])
+
+
+for child in root_trafo.iter():
+    if child.tag == 'MatrixTransformation':
+        mat.append(child.attrib)
+
+M = np.eye(4)
+M_list = list()
+        
+for matrix in mat:
+    thismat = np.eye(4)
+    thismat[0,0] = matrix['m00']
+    thismat[0,1] = matrix['m01']
+    thismat[0,2] = matrix['m02']
+    thismat[0,3] = matrix['m03']
+    thismat[1,0] = matrix['m10']
+    thismat[1,1] = matrix['m11']
+    thismat[1,2] = matrix['m12']
+    thismat[1,3] = matrix['m13']
+    thismat[2,0] = matrix['m20']
+    thismat[2,1] = matrix['m21']
+    thismat[2,2] = matrix['m22']
+    thismat[2,3] = matrix['m23']
+    thismat[3,0] = matrix['m30']
+    thismat[3,1] = matrix['m31']
+    thismat[3,2] = matrix['m32']
+    thismat[3,3] = matrix['m33']
+    
+    M_list.append(thismat)
+    
+    M = np.dot(M.T,thismat)
+    
+
+
+# extract registration point positions
+
+
+p_idx = list()
+pts = list()
+
+for child in root_em.iter():
+    pt = np.zeros(2)
+    if child.tag == 'position':
+        
+        for coords in child.getiterator():            
+            if coords.tag == 'pos_x':
+                pt[0] = float(coords.text)
+            elif coords.tag == 'pos_y':
+                pt[1] = float(coords.text)
+            #elif coords.tag == 'pos_z':
+            #    pt[2] = float(coords.text)
+            
+        pts.append(pt)
+            
+    elif child.tag == 'name':
+        p_idx.append(int(child.text[child.text.rfind(' '):]))
+                
+    
+### TODO ##
+
+
+                
+                
+
 # create new file by copying the header of the input file
 newnavf = navfile[:-4] + '_icy.nav'