Merge branch 'icy' into 'master'

Icy

See merge request schorb/pyem!2

applications/clem_icy.py

+# -*- coding: utf-8 -*-
+# import the py-EM module and make its functions available
+import pyEM as em
+
+import xml.etree.ElementTree as ET
+
+
+
+# parse command line parameters
+
+
+import sys
+import os
+
+
+
+
+
+
+
+
+def pts2xml(imfile,pts):
+    
+    xml_out = os.path.splitext(imfile)[0]+'.xml'
+        
+    root = ET.Element('root')
+    
+    name = ET.SubElement(root, 'name')
+    name.text = os.path.splitext(os.path.basename(imfile))[0]
+    
+    rois = ET.SubElement(root, 'rois')
+    
+    ol = ET.SubElement(root, 'overlays')
+    
+    for pt in pts:
+        roi = ET.SubElement(rois, 'roi')
+        
+        cn = ET.SubElement(roi, 'classname')
+        cn.text = 'plugins.kernel.roi.roi3d.ROI3DPoint'
+        
+        p_id = ET.SubElement(roi, 'id')
+        p_id.text = pt[1]
+        
+        col = ET.SubElement(roi, 'color')
+        col.text = '-48641'
+        
+        sn = ET.SubElement(roi, 'showName')
+        sn.text = 'true'       
+                
+        pname = ET.SubElement(roi, 'name')
+        pname.text = 'Point '+ pt[1]
+        
+        z = ET.SubElement(roi, 'z')
+        z.text = '0'
+        
+        pos = ET.SubElement(roi, 'position')
+        x = ET.SubElement(pos, 'pos_x')
+        x.text = str(pt[0][0])
+        y = ET.SubElement(pos, 'pos_y')
+        y.text = str(pt[0][1])
+
+    
+    em.indent_xml(root)
+    tree = ET.ElementTree(root)
+    tree.write(xml_out)
+
+
+
+
+
+
+
+#%%
+
+navfile = sys.argv[1]
+
+#%%
+
+
+# load the navigator file
+navlines = em.loadtext(navfile)
+allitems = em.fullnav(navlines)
+
+outitems = list(allitems)
+
+
+
+# select "ACQUIRE"
+acq = em.nav_selection(allitems)
+
+# check that only two proper maps are selected
+if not len(acq) == 2: raise ValueError('Select two maps as items to acquire.')
+if not any('Imported' in item.keys() for item in acq):  raise ValueError('One map needs to be imported.')
+
+for item in acq :
+    if 'Imported' in item.keys():
+        m_fm = item
+        mm_fm = em.mergemap(item)
+    else:
+        m_em = item
+        mm_em = em.mergemap(item)
+
+# Find all relevant registration pts
+
+fm_regpts = em.nav_find(allitems,key='DrawnID',val=m_fm['MapID'])
+fm_regpts = em.nav_find(fm_regpts,key='RegPt')
+
+fm_px = []
+for regpt in fm_regpts:
+    fm_px.append([em.get_pixel(regpt,mm_fm),regpt['RegPt'][0]])
+    outitems.remove(regpt)
+
+em_regpts = em.nav_find(allitems,key='DrawnID',val=m_em['MapID'])
+em_regpts = em.nav_find(em_regpts,key='RegPt')
+
+em_px = []
+for regpt in em_regpts:
+    em_px.append([em.get_pixel(regpt,mm_em),regpt['RegPt'][0]])
+    outitems.remove(regpt)
+
+
+pts2xml(mm_fm['mapfile'], fm_px)
+pts2xml(mm_em['mergefile'], em_px)
+
+# create new file by copying the header of the input file
+newnavf = navfile[:-4] + '_icy.nav'
+
+em.write_navfile(newnavf,outitems,xml=False)
+    

applications/sortnav.py

@@ -4,19 +4,15 @@ import pyEM as em
 
 # parse command line parameters
 
-#import argparse
-
-#parser = argparse.ArgumentParser(description='Sort navigator file.')
-#parser.add_argument('navfile', metavar='navfile', type=str, help='a navigator file location')
-
-#args = parser.parse_args()
-
-#navfile = args.navfile
 
 import sys
 
+#%%
+
 navfile = sys.argv[1]
 
+#%%
+
 
 # load the navigator file
 navlines = em.loadtext(navfile)

pyEM.py

@@ -1427,20 +1427,23 @@ def pts2nav(im,pts,cntrs,curr_map,targetitem,nav,sloppy=False,maps=False):
 
 # ------------------------------------------------------------
   
-def nav_find(allitems,key,val):
+def nav_find(allitems,key,val=[]):
 # returns the navigator/mdoc entries with the given key/value pair
 # takes an input navigator (list of dicts), a target key (item property) and the desired values to match    
 # output is the list of navigator items    
          
     filtered = list(filter(lambda item:item.get(key),allitems))
     
-    # deals with integer, string or list entries
-    if type(val)==int: val=str(val)
-    if not key == '# Item':
-        if type(val)==str: val=[val]
-    
-    found = list(filter(lambda item:item[key]==val,filtered))
-       
+    if val==[]:
+        found = filtered
+    else:
+        # deals with integer, string or list entries
+        if type(val)==int: val=str(val)
+        if not key == '# Item':
+            if type(val)==str: val=[val]
+        
+        found = list(filter(lambda item:item[key]==val,filtered))
+           
 
     if not found == []:
         newnav=found

setup.py

@@ -6,7 +6,7 @@ with open("readme.md", "r") as fh:
     long_description = fh.read()
 
 setup(name='py-EM',
-      version='20200603',
+      version='20200609',
       py_modules=['pyEM'],
       description='Tools to interact with Serial EM enabling automated transmission electron microscopy.',
       long_description=long_description,