Added initial version of a rescaling script for mrc volumes, used for...

Added initial version of a rescaling script for mrc volumes, used for rescaling masks and references during STA.

subtomogramAveraging/rescaleMOTL.py

 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-Created on Wed May 15 09:22:40 2019
+Created on Wed Aug 28, 2019
 
 @author: adrian
 """
@@ -20,7 +20,7 @@ parser = argparse.ArgumentParser(description = "Rescales shifts in motif lists (
 parser.add_argument('-o', '--oldMrc', nargs='?', default='.', help='Old tomogram mrc that the MOTLs have been calculated with.')
 parser.add_argument('-n', '--newMrc', nargs='?', default='.', help='New tomogram mrc file that the MOTLs should be scaled to.')
 parser.add_argument('-sf', '--scaleFactor', nargs='?', type=float, help='Manual scale factor, default 2 if nothing specified.')
-parser.add_argument('-s', '--suffix', nargs='?', type=str, default='rescaled', help='Suffix to append to rescaled MOTLs. Default is "_rescaled".')
+parser.add_argument('-s', '--suffix', nargs='?', type=str, default='rescaled', help='Suffix to append to rescaled MOTLs. Default is "rescaled".')
 parser.add_argument('-f', '--force', action='store_true', help='Force overwriting output files.')
 parser.add_argument('-hl', '--numHeaderLines', nargs='?', type=int, default=1, help='Number of header lines in MOTL, default 1.')
 parser.add_argument('file', type=str, nargs='+')

subtomogramAveraging/rescaleVolume.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Aug 29, 2019
+
+@author: adrian
+"""
+
+import mrcfile
+import scipy
+import scipy.ndimage.interpolation
+import sys,os
+import argparse
+
+parser = argparse.ArgumentParser(description = "Rescales shifts in motif lists (MOTLs) generated in PEET with either with a specified scale factor or between two supplied mrc files.")
+
+# parser.add_argument("-f", "--file", help="create overlay for a single file",
+parser.add_argument('-o', '--oldMrc', nargs='?', default='.', help='Old tomogram mrc that the MOTLs have been calculated with.')
+parser.add_argument('-n', '--newMrc', nargs='?', default='.', help='New tomogram mrc file that the MOTLs should be scaled to.')
+parser.add_argument('-sf', '--scaleFactor', nargs='?', type=float, help='Manual scale factor, default 2 if nothing specified.')
+parser.add_argument('-s', '--suffix', nargs='?', type=str, default='rescaled', help='Suffix to append to rescaled MOTLs. Default is "rescaled".')
+parser.add_argument('-f', '--force', action='store_true', help='Force overwriting output files.')
+parser.add_argument('-hl', '--numHeaderLines', nargs='?', type=int, default=1, help='Number of header lines in MOTL, default 1.')
+parser.add_argument('file', type=str, nargs='+')
+
+args = parser.parse_args()
+
+if not args.force:
+    args.force = False
+
+if args.scaleFactor == None:
+    if not args.oldMrc == '.' and not args.newMrc == '.':
+        mrc1 = mrcfile.mmap('/home/nieverge/Adrian_PEET/an9_g5_t1_mc2_ipp_icon_flip_b4.rec', mode='r+')
+        mrc2 = mrcfile.mmap('/home/nieverge/Adrian_PEET/an9_g5_t1_mc2_ipp_icon_flip_b2.rec', mode='r+')
+
+        # print(mrc1.header)
+
+        # scale factor is the ratio at which the pixel/nm get scaled between the first and the second mrc.
+        scaleFactor = mrc1.header.cella.x / mrc1.header.mx / (mrc2.header.cella.x / mrc2.header.mx)
+
+        print("Scaling volume by a factor {:.2g}.".format(scaleFactor))
+    else:
+        scaleFactor = 2
+        print("No input and output mrcs specified. Using scale factor %g." % (scaleFactor));
+
+for file in args.file:
+
+    with mrcfile.open(file, 'r') as mrcIn:
+        oldVolume = mrcIn.data
+        rescaledVolume = scipy.ndimage.interpolation.zoom(oldVolume, scaleFactor, order=1)
+
+        print("Resized original volume of {} to {}.".format(mrcIn.data.shape,rescaledVolume.shape))
+
+        basePath = os.path.splitext(file)[0]
+        outMrcPath = "{}_{}.mrc".format(basePath, args.suffix)
+        with mrcfile.new(outMrcPath, overwrite=args.force) as mrcOut:
+            mrcOut.set_data(rescaledVolume)
\ No newline at end of file