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reshape-cut-rotate_working.py

+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+#This script does 2 things:
+#1) It checks for beam dumps during MAP acquisition
+#   In case BMS is < BMS_MIN, it reshapes the map discarding void pixels
+# AND
+#2) It discards half-filled rows/columns in case of manual interruption of the map
+
+import glob
+import h5py
+import itertools
+import numpy as np
+import os
+import sys
+
+from mylib import count_steps, check_bms, orientation
+
+BMS_MIN = 1e-2
+PRECISION = 5
+EXT = "h5"
+PATH_SCALAR = "/Measurement/TransientScalarData"
+PATH_VECTOR = "/Measurement/TransientVectorData"
+NEW_FOLDER = "/cut-reshaped/"
+NEWNAME_APP = "_new.h5"
+
+
+
+def cut_reshape(in_file, out_fold):
+    new_map = os.path.join( out_fold, in_file.split('.h5')[0] + NEWNAME_APP)
+    
+    with h5py.File(in_file, 'r') as f:
+    
+        move_hor = False
+        for run in f.keys():
+            print ("Run: %s" %run)
+            
+            x = f[run+PATH_SCALAR+"/X"][...]
+            y = f[run+PATH_SCALAR+"/Y"][...]
+            
+        # when X moves first, in order to see the map on PyMCA, the number of 
+        # columns to enter is the number of rows. The map will appear rotated.             
+            try:
+                x, y, move_hor = orientation(x, y)
+            except ValueError:
+                print('x x x Size not valid for map. Please check file. x x x \n\n\n')
+                break
+
+            shape_x, shape_y = count_steps(x,y)    # was (y,x) because x is vertical axis on IAEA gui; changed now
+            total_points = shape_x * shape_y
+            
+            print("Original map size: (%d,%d), total point=%d" % (shape_x, shape_y, total_points) )
+
+            # each pixel has several bms value: checking the minimum only
+            bms = f[run+PATH_VECTOR+"/BMS-T"][...]
+            bms = bms.min(axis=1)
+            beam_lost, valid_pixels = check_bms(bms)
+            
+            if valid_pixels == 0:
+                print('x x x x x x x No valid pixels, moving on.\n\n\n')
+                break
+
+            if move_hor:
+                col = shape_y
+                row = np.round(valid_pixels/shape_y)
+                
+            else:
+                row = shape_x
+                col = np.round(valid_pixels/shape_x)
+                    
+            if valid_pixels < shape_x*shape_y:
+                print('Valid pixels =', valid_pixels)
+                print('Original map =', shape_x*shape_y)
+                
+                if move_hor:
+                    row = valid_pixels/shape_y
+                else:
+                    col = valid_pixels/shape_x
+                    
+            if beam_lost:
+                print('Beam dump detected!')                
+                print('Original size:', shape_x, shape_y)
+                print('New size:', row, col)
+            
+            if (row*col==shape_x*shape_y):
+                print('This map is ok! No cutting, just reshaping!\n')
+                print('Original size:', shape_x, shape_y)
+                print('New size:', row, col)
+             
+
+
+            with h5py.File(new_map, 'w') as fout:
+                total_point = row * col
+                # print("Map size: (%d,%d), total point=%d\n" % (row, col, total_point))
+                
+                print('\n--> Now reshaping TransientVectorData:')
+                for vectorData in f[run+PATH_VECTOR].keys():
+                    #print (vectorData)
+                    v = f[run+PATH_VECTOR+"/"+vectorData][...]
+                    v = v[0:total_point]
+                    v = v.reshape((row,col,v.shape[-1]))
+                    if move_hor:
+                       print('Rotating map here to facilitate data viewing on PyMCA.')                       
+                       v = np.rot90(v, -1, axes=(1,0))
+                       print(v.shape)
+                    #print("New shape = ", v.shape)
+                    fout.create_dataset(run+PATH_VECTOR+"/"+vectorData, data=v, compression = "gzip", shuffle=True)
+                print('\n--> Done! Now reshaping TransientScalarData:')
+                
+                for scalarData in f[run+PATH_SCALAR].keys():
+                    #print(scalarData)
+                    s = f[run+PATH_SCALAR+"/"+scalarData][...]
+                    s = s[0:total_point]
+                    if s.shape[0] == total_point:
+                        s = s.reshape(row, col)                    
+                    if move_hor:
+                        s = np.rot90(s, -1, axes=(1,0))
+
+                    #print("New shape: ",s.shape)
+                    fout.create_dataset(run+PATH_SCALAR+"/"+scalarData, data=s)
+    
+                
+
+
+####################################################################
+
+def run():
+    print('-------------------------------------------------\n')
+    print('---------           Welcome!         ------------\n')
+    print("---        Let's cut your XRF maps!           ---\n")
+    print('-------------------------------------------------\n')
+    
+    in_path = './'
+    out_path = in_path + NEW_FOLDER
+    # if out_path is read only, uncomment next line
+    # out_path = str(input('Where do you want to save the reshaped maps?' ))
+    
+    # checks automatically all the h5 files in the in_path 
+    file_list = glob.glob('{0}/*'.format(in_path)+EXT)
+    print('I found '+str(len(file_list))+' files matching the extension '+EXT)
+    print(file_list)
+    print('\n')
+    
+    if len(file_list) == 0:
+        print("--> Can't do much with 0 files! Sorry!")
+        print("--> Move the maps in the same folder as the program and try again!")
+    
+    else: 
+        print("--> All these files will be cut and reshaped. \n")
+        print("--> Don't worry: overwriting is not an option. ;) \n\n\n")
+        
+        if not os.path.exists(out_path):
+            os.makedirs(out_path)
+        
+        for filename, i in zip(file_list, range(len(file_list))):
+            filename = filename[2:]
+            cut_reshape(filename, out_path)
+            print('\n - - - - Map {0}/{1} successfully checked.\n'.format(i+1, len(file_list)))
+
+    print('\n --> Have a nice day!')
+
+if __name__ == "__main__":
+    run()