From 10d2579cfeea3c616b4785da28953e140b56b25c Mon Sep 17 00:00:00 2001
From: Mamad Eshraqi <mohammad.eshraqi@esss.se>
Date: Mon, 9 Jul 2018 14:49:11 +0200
Subject: [PATCH] A binary fieldmap batch conversion and trimming script is
added. the conversion is now available also in TraceWin, but the rimming is
still useful, specially if we add the other axes.
---
.../Batch_Convert_and_Cut_Binary_Fieldmap.py | 206 ++++++++++++++++++
1 file changed, 206 insertions(+)
create mode 100644 examples/Binary_fieldmap/Batch_Convert_and_Cut_Binary_Fieldmap.py
diff --git a/examples/Binary_fieldmap/Batch_Convert_and_Cut_Binary_Fieldmap.py b/examples/Binary_fieldmap/Batch_Convert_and_Cut_Binary_Fieldmap.py
new file mode 100644
index 0000000..d92d1b0
--- /dev/null
+++ b/examples/Binary_fieldmap/Batch_Convert_and_Cut_Binary_Fieldmap.py
@@ -0,0 +1,206 @@
+'''
+Now that TraceWin can also convery binary fieldmaps to ASCII the main usage is reduced to trimming fieldmaps
+-- M. Eshraqi 2018 July 09
+
+
+
+The field map file syntax is the following in the BINARY format:
+- Dimension 1 :
+ nz (integer 4 bytes) zmax (double 8 bytes) Norm (double 8 bytes)
+ for k=0 to nz
+ Fz(k.zmax/nz) (float 4 bytes)
+
+- Dimension 2 :
+ nz (integer 4 bytes) zmax (double 8 bytes) nx (integer 4 bytes) xmax (double 8 bytes) Norm (double 8 bytes)
+ for k=0 to nz
+ for i=0 to nr
+ Fz(k*zmax/nz, i*rmax/nr) (float 4 bytes)
+
+- Dimension 3 :
+(Be careful to the dimention order)
+ nz (integer 4 bytes) zmax (double 8 bytes)
+ nx (integer 4 bytes) xmin (double 8 bytes) xmax (double 8 bytes)
+ ny (integer 4 bytes) ymin (double 8 bytes) ymax (double 8 bytes)
+ Norm (double 8 bytes)
+ for k=0 to nz
+ for j=0 to ny
+ for i=0 to nx
+ Fz(k*zmax/nz, ymin+j*(ymax-ymin)/ny, xmin+i*(xmax-xmin)/nx) (float 4 bytes)
+Warning: The lattice has to be regular.
+The normalization factor is equal to ke/Norm or kb/Norm.
+Fz are in MV/m for electric field or in T for magnetic field. The dimensions are in meter.
+'''
+
+import os
+import numpy as np
+#import pandas as pd
+
+def read_binary_fieldmap(path_plus_file, fieldmap_dim):
+ '''
+ takes a filename for a binary fieldmap and dimension of the fieldmap,
+ 1D = 1, 2D = 2, 3D = 3
+ and returns a numpy array, with the same format as the TraceWin fieldmap, without the header in ASCII
+ '''
+
+ File = open(os.path.join(mypath, f),'r')
+ #print(f)
+
+ if fieldmap_dim == 3:
+ Header_Type = np.dtype([('Nz', 'int32'), ('Zmax', 'float64'), ('Nx','int32'), ('Xmin', 'float64'), ('Xmax', 'float64'),
+ ('Ny','int32'), ('Ymin','float64'), ('Ymax','float64'), ('Norm', 'float64')])
+ THeader = np.fromfile(File, dtype=Header_Type, count=1)
+ Nz = THeader['Nz'][0]
+ Zmax = THeader['Zmax'][0]
+ Nx = THeader['Nx'][0]
+ Xmin = THeader['Xmin'][0]
+ Xmax = THeader['Xmax'][0]
+ Ny = THeader['Ny'][0]
+ Ymin = THeader['Ymin'][0]
+ Ymax = THeader['Ymax'][0]
+ Norm = THeader['Norm'][0]
+ Header = np.zeros(len(THeader))
+ Header = np.array([Nz, Zmax, Nx, Xmin, Xmax, Ny, Ymin, Ymax, Norm])
+ elif fieldmap_dim == 2:
+ Header_Type = np.dtype([('Nz', 'int32'), ('Zmax', 'float64'), ('Nx','int32'), ('Xmax', 'float64'),
+ ('Norm', 'float64')])
+ Header = np.fromfile(File, dtype=Header_Type, count=1)
+ Nz = THeader['Nz'][0]
+ Zmax = THeader['Zmax'][0]
+ Nx = THeader['Nx'][0]
+ Xmax = THeader['Xmax'][0]
+ Norm = THeader['Norm'][0]
+ Header = np.zeros(len(THeader))
+ elif fieldmap_dim == 1:
+ Header_Type = np.dtype([('Nz', 'int32'), ('Zmax', 'float64'), ('Norm', 'float32')])
+ Header = np.fromfile(File, dtype=Header_Type, count=1)
+ Nz = THeader['Nz'][0]
+ Zmax = THeader['Zmax'][0]
+ Norm = THeader['Norm'][0]
+ Header = np.zeros(len(THeader))
+
+ Field_Type = np.dtype([('F_val','float32')])
+
+ Nf = int(Nz+1)
+ if fieldmap_dim == 2:
+ Nf *= int(Nx+1)
+ elif fieldmap_dim == 3:
+ Nf *= (int(Ny+1)*int(Nx+1))
+ #print(Nf)
+
+ Field = np.fromfile(File, dtype=Field_Type, count=Nf)
+
+ #print(Field)
+ #plot(Field)
+ return Header, Field
+
+def cut_fieldmap_length(Field, Header, fieldmap_dim, entrance_rows_cut, exit_rows_cut):
+ '''
+ Takes a Field (ASCII numpy array with TraceWin fieldmap data format),
+ dimesion of the fieldmap,
+ number of data rows to be removed from array from the entrance side of the field, and
+ number of data rows to be removed from array from the exit side of the field
+ and returns a numpy array which contains only the remaining rows.
+ '''
+ #print(Header[0])
+ lowx = np.arange(0,int(entrance_rows_cut))
+ #print('lowx', lowx)
+ highx = np.arange(int(Header[0]+1-exit_rows_cut), int(Header[0]+1))
+ #print('highx', highx)
+ newNz = (Header[0]+1)-entrance_rows_cut-exit_rows_cut
+ stepZ = Header[1] / Header[0]
+
+ if fieldmap_dim == 1:
+ newlength = newNz
+ elif fieldmap_dim == 2:
+ Fieldmapmatrix = np.reshape(Field, (int(Header[0]+1), int(Header[2]+1)))
+ newlength = newNz*(Header[2]+1)
+ elif fieldmap_dim == 3:
+ Fieldmapmatrix = np.reshape(Field, (int(Header[0]+1), int((Header[2]+1)*(Header[5]+1))))
+ #print(Fieldmapmatrix.shape)
+ newlength = newNz*(Header[2]+1)*(Header[5]+1)
+
+ if (entrance_rows_cut>0 and exit_rows_cut>0):
+ x = np.delete(Fieldmapmatrix,(lowx, highx), axis=0)
+ elif (entrance_rows_cut ==0):
+ x = np.delete(Fieldmapmatrix,(highx), axis=0)
+ elif exit_rows_cut ==0:
+ x = np.delete(Fieldmapmatrix,(lowx), axis=0)
+
+ ShortenedMatrix = np.reshape(x, (int(newlength), 1))
+
+ Header[0] = newNz-1
+ Header[1] = stepZ*(newNz-1)
+
+ return Header, ShortenedMatrix
+
+'''
+The parameters in the following six rows define the path to your fieldmap, no name is needed, this script
+scans the folder and converts all files, assumes all are binary fieldmaps, to ASCII fieldmaps.
+The dimension of the field is also needed.
+If you need to cut the field, the n_enter and n_exit should be adjusted.
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
+# #
+# C h a n g e t h e f o l l o w i n g v a l u e s #
+# #
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
+'''
+
+mypath = 'Data/FM/' # where the fieldmaps are stored
+fieldmap_dim = 3
+#fieldmap_dim = 2
+#fieldmap_dim = 1
+n_enter = 0 #Number of lines to be removed from entrance of fieldmap
+n_exit = 0 #Number of lines to be removed from exit of fieldmap
+
+onlyfiles = [f for f in os.listdir(mypath) if os.path.isfile(os.path.join(mypath, f))]
+
+for f in onlyfiles:
+ if f[0]!=".":
+ Header, Field = read_binary_fieldmap(f, fieldmap_dim)
+
+ if (n_enter+n_exit>0):
+ Header, Field = cut_fieldmap_length(Field, Header, fieldmap_dim, n_enter, n_exit)
+
+ with open(os.path.join(mypath, 'ASCII', f), 'w') as out_file:
+
+ stepZ = Header[1] / Header[0] #stepZ = Zmax / Nz
+
+ out_file.write(' '.join(str(hval) for hval in Header[0:2]))
+ out_file.write('\n')
+ if fieldmap_dim == 1:
+ #Norm = Header[2]
+
+ #out_file.write(' '.join(str(hval) for hval in Header[0:2]))
+ #out_file.write('\n')
+ out_file.write(' '.join(str(Header[2])))
+ out_file.write('\n')
+
+ elif fieldmap_dim == 2:
+ #Norm = Header[4]
+ stepX = Header[3]/Header[2] #stepX = Xmax / Nx
+
+ #out_file.write(' '.join(str(hval) for hval in Header[0:2]))
+ #out_file.write('\n')
+ out_file.write(' '.join(str(hval) for hval in Header[2:4]))
+ out_file.write('\n')
+ out_file.write(' '.join(str(Header[4])))
+ out_file.write('\n')
+
+ elif fieldmap_dim == 3:
+ #Norm = Header[8]
+ stepX = (Header[4]-Header[3])/Header[2] #stepX = (Xmax - Xmin) / Nx
+ stepY = (Header[7]-Header[6])/Header[5] #stepY = (Ymax - Ymin) / Ny
+
+ #out_file.write((' '.join(str(hval) for hval in Header[0:2])))
+ #out_file.write('\n')
+ out_file.write((' '.join(str(hval) for hval in Header[2:5])))
+ out_file.write('\n')
+ out_file.write((' '.join(str(hval) for hval in Header[5:8])))
+ out_file.write('\n')
+ out_file.write(''.join(str(Header[8])))
+ out_file.write('\n')
+
+ for fval in Field:
+ out_file.write(str(fval[0][0]))
+ out_file.write('\n')#print(fval)
\ No newline at end of file
--
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