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Commit d67eaeca authored by Ilaria Carlomagno's avatar Ilaria Carlomagno
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Added comment in the hdf5 file

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reshape-cut-rotate_working.py
+ 45
− 45
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......@@ -33,7 +33,8 @@ def cut_reshape(in_file, out_fold):
with h5py.File(in_file, 'r') as f:
move_ver = False
comment_line = ''
for run in f.keys():
date_str = 'Run%Y%m%d %H%M%S'
# the first part of the string contains date and time of acquisition
......@@ -42,8 +43,8 @@ def cut_reshape(in_file, out_fold):
sample_name = run[19:]
new_map = './'+ NEW_FOLDER + sample_name + date_acq.strftime('_%Y-%m-%d_%H-%M-%S')
print ("Sample_name: %s." %sample_name)
print (date_acq.strftime('\tAcquisition time: %d/%m/%Y - %H:%M:%S.'))
print("Sample_name: %s." %sample_name)
print(date_acq.strftime('\tAcquisition time: %d/%m/%Y - %H:%M:%S.'))
try:
x = f[run+PATH_SCALAR+"/X"][...]
......@@ -59,7 +60,7 @@ def cut_reshape(in_file, out_fold):
# The following section fixes this issue. The output file will be shown
# in the correct orientation on PyMCA.
try:
x, y, move_ver = orientation(x, y)
x, y, move_ver = orientation(x, y)
except ValueError:
print('\tx x x x x x x x x x x x x x x x x x x x x x x x')
print('\tx Size not valid for map. Please check file. x ')
......@@ -85,6 +86,7 @@ def cut_reshape(in_file, out_fold):
row = shape_x
col = math.floor(valid_pixels/shape_x)
new_map += '_rot'
comment_line += 'This map has been rotated.\n'
else:
col = shape_y
row = math.floor(valid_pixels/shape_y)
......@@ -93,50 +95,49 @@ def cut_reshape(in_file, out_fold):
print(' !\tValid pixels = %s out of %s' %(valid_pixels, shape_x*shape_y))
if not beam_lost:
print('\tIncomplete map collection found.')
comment_line += 'Incomplete map collection found'
print('\tNew map shape: (%d, %d)' %(row, col))
new_map += '_cut'
if (row*col==shape_x*shape_y):
print('\tNo cutting, just reshaping.\n')
comment_line += 'This map was not cut. Only reshaping has been done.'
print('\tNew map shape: (%d, %d)' %(row, col))
new_map += '.h5'
with h5py.File(new_map, 'w') as fout:
final_points = row * col
my_comment = 'Test_ciao !!'
fout.create_dataset("Comments", data=my_comment)
# Reshaping TransientVectorData
for vectorData in f[run+PATH_VECTOR].keys():
v = f[run+PATH_VECTOR+"/"+vectorData][...]
v = v[0:final_points]
v = v.reshape(row,col,v.shape[-1])
fout = h5py.File(new_map, 'w')
final_points = row * col
fout.create_dataset("Comments", data=comment_line)
# Reshaping TransientVectorData
for vectorData in f[run+PATH_VECTOR].keys():
v = f[run+PATH_VECTOR+"/"+vectorData][...]
v = v[0:final_points]
v = v.reshape(row,col,v.shape[-1])
# the rotation of the map is done here:
if move_ver:
v = np.rot90(v, -1, axes=(1,0))
fout.create_dataset(run+"/Detector_data/"+vectorData, data=v, compression = "gzip", shuffle=True)
# Reshaping TransientScalarData:')
for scalarData in f[run+PATH_SCALAR].keys():
if scalarData in AcceptedList:
s = f[run+PATH_SCALAR+"/"+scalarData][...]
s = s[0:final_points]
if s.shape[0] == final_points:
s = s.reshape(row, col)
# the rotation of the map is done here:
if move_ver:
v = np.rot90(v, -1, axes=(1,0))
fout.create_dataset(run+"/Detector_data/"+vectorData, data=v, compression = "gzip", shuffle=True)
# Reshaping TransientScalarData:')
for scalarData in f[run+PATH_SCALAR].keys():
if scalarData in AcceptedList:
s = f[run+PATH_SCALAR+"/"+scalarData][...]
s = s[0:final_points]
if s.shape[0] == final_points:
s = s.reshape(row, col)
if move_ver:
s = np.rot90(s, -1, axes=(1,0))
fout.create_dataset(run+"/Motor_positions/"+scalarData, data=s)
# Reshaping Positioners (i.e. motor position before map collection)
for motor_position in f[run+POSITIONERS].keys():
p = f[run+POSITIONERS+"/"+motor_position][...]
fout.create_dataset(run+"/Starting_positions/"+motor_position, data=p)
s = np.rot90(s, -1, axes=(1,0))
fout.create_dataset(run+"/Motor_positions/"+scalarData, data=s)
# Reshaping Positioners (i.e. motor position before map collection)
for motor_position in f[run+POSITIONERS].keys():
p = f[run+POSITIONERS+"/"+motor_position][...]
fout.create_dataset(run+"/Starting_positions/"+motor_position, data=p)
####################################################################
......@@ -161,15 +162,14 @@ def run():
if len(file_list) == 0:
print("\t-> Can't do much with 0 files! Sorry!")
print("\t-> Move the maps in the same folder as the program and try again!")
print("\t-> Move the maps in the same folder as the program and try again!")
else:
print("\t-> All the files mentioned above will be cut and reshaped.")
print("\t-> Don't worry: overwriting raw data is not an option. ;) \n")
print("\t-> Don't worry: overwriting raw data is not an option. ;) \n")
if not os.path.exists(out_path):
os.makedirs(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)
......@@ -178,4 +178,4 @@ def run():
print('\tHave a nice day.\n')
if __name__ == "__main__":
run()
\ No newline at end of file
run()
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