PR fixes V: use metadata to write coordinates file

Author: fede-pe

xmipptomo/utils.py

@@ -302,16 +302,7 @@ def writeOutputTiltSeriesCoordinates3dXmdFile(soc, filePath, sr, halfX, halfY, t
      its tomo tsId). If no tsId is input the xmd output file will contain all the coordinates belonging to the
      set. """
 
-    xmdHeader = "# XMIPP_STAR_1 *\n" \
-                "#\n" \
-                "data_noname\n" \
-                "loop_\n" \
-                " _xcoor\n" \
-                " _ycoor\n" \
-                " _zcoor\n"
-
     coordinatesInfo = []
-    fieldNames = ['x', 'y', 'z']
 
     if tsId is None:
         for coord in soc:
@@ -328,14 +319,22 @@ def writeOutputTiltSeriesCoordinates3dXmdFile(soc, filePath, sr, halfX, halfY, t
     if len(coordinatesInfo) == 0:
         return False
 
-    with open(filePath, 'w') as f:
-        f.write(xmdHeader)
-        writer = csv.DictWriter(f, delimiter='\t', fieldnames=fieldNames)
+    print(coordinatesInfo)
 
-        for ci in coordinatesInfo:
-            writer.writerow({'x': ci[0],
-                             'y': ci[1],
-                             'z': ci[2]})
+    mdCoor = lib.MetaData()
+
+    for ci in coordinatesInfo:
+        nRow = md.Row()
+        print(ci)
+        print(ci[0])
+        print(type(ci[0]))
+        nRow.setValue(lib.MDL_XCOOR, int(ci[0]))
+        nRow.setValue(lib.MDL_YCOOR, int(ci[1]))
+        nRow.setValue(lib.MDL_ZCOOR, int(ci[2]))
+
+        nRow.addToMd(mdCoor)
+
+    mdCoor.write(filePath)
 
     return True
 
@@ -520,7 +519,6 @@ def writeMdCoordinates(setOfCoordinates, tomo, fnCoor):
     return fnCoor
 
 
-
 def parseLandmarkCoordinatesFile(lmFile):
     """ This function retrive a list of landmark coordinates form xmd file as generated by xmipp program
     xmipp_tomo_detect_landmarks"""