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refactored + removed call of readCalibParametersInFile() in convert2c…
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…orfile()
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@BM32ESRF
BM32ESRF committed Oct 23, 2024
1 parent f0ed771 commit a946eda
Showing 1 changed file with 78 additions and 52 deletions.
130 changes: 78 additions & 52 deletions LaueTools/LaueGeometry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1752,7 +1752,7 @@ def matxmas_to_matstarlab(satocr, calib):

def Compute_data2thetachi(filename:str, sorting_intensity="yes", detectorparams=None,
kf_direction="Z>0",
verbose=1,
verbose=0,
pixelsize:float=165.0 / 2048,
dim=(2048, 2048),
saturation=0,
Expand Down Expand Up @@ -1801,11 +1801,12 @@ def Compute_data2thetachi(filename:str, sorting_intensity="yes", detectorparams=
alldata, nbpeaks = IOLT.readfile_dat(filename, returnnbpeaks=True)
listcolumnsname = IOLT.getcolumnsname_dat(filename)
nbcolumns = len(listcolumnsname)

print('\n In Compute_data2thetachi(): filename :', filename)
print('nbpeaks', nbpeaks)
print('alldata.shape', alldata.shape)
print('raw nbcolumns', nbcolumns)

if verbose:
print('\n In Compute_data2thetachi(): filename :', filename)
print('nbpeaks', nbpeaks)
print('alldata.shape', alldata.shape)
print('raw nbcolumns', nbcolumns)

# take all columns (spots properties)
dict_spotsproperties = IOLT.getspotsproperties_dat(filename)
Expand All @@ -1819,7 +1820,7 @@ def Compute_data2thetachi(filename:str, sorting_intensity="yes", detectorparams=
elif nbpeaks == 1:
data_xyI = np.take(alldata, basic_colunms_idx, axis=0)

print("data_spotsproperties.shape", data_spotsproperties.shape)
if verbose: print("data_spotsproperties.shape", data_spotsproperties.shape)

if saturation:
data_Ipixmax = alldata[:, -1]
Expand Down Expand Up @@ -1963,7 +1964,7 @@ def Compute_data2thetachi(filename:str, sorting_intensity="yes", detectorparams=
return twicetheta, chi, dataintensity, data_x, data_y, dict_spotsproperties

def convertdat2corfile(filename_dat:str, fullpath_det:str, dirname_in:str=None,
dirname_out:str=None):
dirname_out:str=None, verbose=0):
"""
Write a .cor file from a .dat file (peaksearch made peaks list) taking into account a .det file (calibration file)
Expand Down Expand Up @@ -2003,14 +2004,16 @@ def convertdat2corfile(filename_dat:str, fullpath_det:str, dirname_in:str=None,
raise KeyError('Can not read pixel size in file : %s'%fullpath_det)

if 'CCDCalibParameters' in CCDCalibdict:
calibparam = CCDCalibdict['CCDCalibParameters']
list5paramscalib = CCDCalibdict['CCDCalibParameters']

#dict_spotsproperties = IOLT.getspotsproperties_dat(datfilename_in)

print('pixelsize',pixelsize)
print('CCDCalibdict',CCDCalibdict)
if verbose:
print('In convertdat2corfile() :')
print('pixelsize',pixelsize)
print('CCDCalibdict',CCDCalibdict)

filename_out = convert2corfile(datfilename_in, calibparam, dirname_in=None,
filename_out = convert2corfile(datfilename_in, list5paramscalib, dirname_in=None,
dirname_out=dirname_out,
pixelsize=pixelsize,
CCDCalibdict=CCDCalibdict, add_props=False,
Expand All @@ -2020,78 +2023,84 @@ def convertdat2corfile(filename_dat:str, fullpath_det:str, dirname_in:str=None,
return filename_out


def convert2corfile(filename, calibparam, dirname_in=None,
dirname_out=None,
pixelsize=165.0 / 2048,
CCDCalibdict=None, add_props=False,
addspotproperties=False):
def convert2corfile(filename_dat:str, list5paramscalib:list, dirname_in:str=None, dirname_out:str=None,
pixelsize:float=165.0 / 2048,
CCDCalibdict:dict=None, add_props=False,
addspotproperties:bool=False,
verbose:int=0):
r"""
Convert .dat (peaks list from peaksearch procedure) to .cor (adding scattering angles 2theta chi)
From X,Y pixel positions in peak list file (x,y,I,...) and detector plane geometry comptues scattering angles 2theta chi
and creates a .cor file (ascii peaks list (2theta chi X Y int ...))
:param CCDCalibdict: dictionary of CCD file and calibration parameters. If the dictionnary has got keys 'pixelsize' and 'CCDCalibPameters', calibparam and pixelsize are useless!
:param filename_dat: str, filename of fullpath of .dat file. In filename_dat only then provide the path to folder with dirname_in
:param CCDCalibdict: dictionary of CCD file and calibration parameters. If the dictionnary has got keys 'pixelsize' and 'CCDCalibPameters', calicalibdet5parambparam and pixelsize are useless!
:param calibparam: list of 5 CCD calibration parameters (used if CCDCalibdict is None or CCDCalibdict['CCDCalibPameters'] is missing)
:param calibdet5param: list of 5 CCD calibration parameters (used only if CCDCalibdict is None or if CCDCalibdict['CCDCalibPameters'] is missing)
:param pixelsize: CCD pixelsize (in mm) (used if CCDCalibdict is None or if CCDCalibdict['pixelsize'] is missing)
:param add_props: add all peaks properties to .cor file instead of the 5 columns
TODO: remove add_props
"""
if verbose:
print('In convert2corfile(): ')
if dirname_in != None:
filename_in = os.path.join(dirname_in, filename)
fullpathdat_in = os.path.join(dirname_in, filename_dat)
else:
filename_in = filename
fullpathdat_in = filename_dat

#print('using CCDCalibdict in convert2corfile for %s'%filename, CCDCalibdict)

if CCDCalibdict is not None:
if "CCDCalibParameters" in CCDCalibdict:
calibparam = CCDCalibdict["CCDCalibParameters"]
list5paramscalib = CCDCalibdict["CCDCalibParameters"]

if "xpixelsize" in CCDCalibdict:
pixelsize = CCDCalibdict["xpixelsize"]

if "pixelsize" in CCDCalibdict:
pixelsize = CCDCalibdict["pixelsize"]
else:
print('WARNING: using pixelsize given in argument of convert2corfile()')
print('WARNING: using pixelsize and 5 detector geometry parameters given as arguments of convert2corfile()')
pass

#print('using pixelsize: ', pixelsize)

dict_spotsproperties = None
if addspotproperties:
(twicetheta, chi, dataintensity, data_x, data_y, dict_spotsproperties) = Compute_data2thetachi(filename_in,
(twicetheta, chi, dataintensity, data_x, data_y, dict_spotsproperties) = Compute_data2thetachi(fullpathdat_in,
sorting_intensity="yes",
detectorparams=calibparam,
detectorparams=list5paramscalib,
pixelsize=pixelsize,
addspotproperties=True)

print('In convert2corfile(): dict_spotsproperties',dict_spotsproperties)
print(dict_spotsproperties['data_spotsproperties'])
addspotproperties=True,
verbose=verbose)
if verbose:
print('dict_spotsproperties',dict_spotsproperties)
print("dict_spotsproperties['data_spotsproperties']", dict_spotsproperties['data_spotsproperties'])
else:
(twicetheta, chi, dataintensity, data_x, data_y) = Compute_data2thetachi(filename_in,
(twicetheta, chi, dataintensity, data_x, data_y) = Compute_data2thetachi(fullpathdat_in,
sorting_intensity="yes",
detectorparams=calibparam,
detectorparams=list5paramscalib,
pixelsize=pixelsize,
addspotproperties=False)
addspotproperties=False,
verbose=verbose)
if add_props:
if len(twicetheta) > 1:
rawdata, allcolnames = IOLT.read_Peaklist(filename_in, output_columnsname=True)
rawdata, allcolnames = IOLT.read_Peaklist(fullpathdat_in, output_columnsname=True)
# need to sort data by intensity (col 3) 'peak_Isub'
sortedind = np.argsort(rawdata[:, 3])[:: -1]
data = rawdata[sortedind]

add_props = (data[:, 2:], allcolnames[2:])
else:
rawdata, allcolnames = IOLT.read_Peaklist(filename_in, output_columnsname=True)
rawdata, allcolnames = IOLT.read_Peaklist(fullpathdat_in, output_columnsname=True)
add_props = (np.array([rawdata[2:]]), allcolnames[2:])

# TODO: handle windowsOS path syntax
filename_wo_path = filename.split("/")[-1]
path_in, filename_wo_path = os.path.split(fullpathdat_in)

file_extension = filename_wo_path.split(".")[-1]

Expand All @@ -2104,36 +2113,53 @@ def convert2corfile(filename, calibparam, dirname_in=None,

if CCDCalibdict is not None:
for kk, key in enumerate(DictLT.CCD_CALIBRATION_PARAMETERS[:5]):
CCDCalibdict[key] = calibparam[kk]
CCDCalibdict[key] = list5paramscalib[kk]

CCDCalibdict["xpixelsize"] = pixelsize
CCDCalibdict["ypixelsize"] = pixelsize
CCDCalibdict["pixelsize"] = pixelsize

param = CCDCalibdict

# update dict according to values in file .cor
with open(filename_in, "r") as f:
param = IOLT.readCalibParametersInFile(f, Dict_to_update=CCDCalibdict)
# Needed for IndexSpotsSet index() ??
# # TODO: update dict according to values in file .cor. Something wrong filename_in is a .dat file
# assert os.path.split(filename_in)[-1].endswith(('.cor','.det'))

# with open(filename_in, "r") as f:
# param = IOLT.readCalibParametersInFile(f, Dict_to_update=CCDCalibdict)

else:
param = calibparam + [pixelsize]
param = list5paramscalib + [pixelsize]

# print('add_props', data.shape, add_props)
IOLT.writefile_cor(filename_out, twicetheta, chi, data_x, data_y, dataintensity,
finalcorfilename = IOLT.writefile_cor(filename_out, twicetheta, chi, data_x, data_y, dataintensity,
data_props=add_props,
sortedexit=False,
param=param,
initialfilename=filename,
dict_data_spotsproperties=dict_spotsproperties)
param=param, # can be list of dict
initialfilename=filename_dat,
dict_data_spotsproperties=dict_spotsproperties,
dirname_output=dirname_out,
verbose=verbose)
if verbose:
print('In convert2corfile() at the end: ')
print('Writing .cor file in ',finalcorfilename)
if dirname_out is not None:
path_out =dirname_out
elif dirname_in is not None:
path_out = dirname_in
else:
path_out = path_in
print('in folder', path_out)

return finalcorfilename


def convert2corfile_fileseries(fileindexrange, filenameprefix, calibparam, suffix="",
nbdigits=4,
dirname_in=None,
dirname_out=None,
pixelsize=165.0 / 2048,
fliprot="no"):
def convert2corfile_fileseries(fileindexrange:list, filenameprefix:str, calibparam:list, suffix="",
nbdigits:int=4,
dirname_in:str=None,
dirname_out:str=None,
pixelsize:float=165.0 / 2048,
fliprot:str="no"):
r"""
convert a serie of peaks list ascii files to .cor files (adding scattering angles).
Expand All @@ -2144,7 +2170,7 @@ def convert2corfile_fileseries(fileindexrange, filenameprefix, calibparam, suffi
:param nbdigits: nb of digits of file index in filename (with zero padding)
(example: for myimage_0002.ccd nbdigits = 4
:param calibparam: list of 5 CCD cakibration parameters
:param calibparam: list of 5 CCD calibration parameters
"""
encodingdigits = "%%0%dd" % nbdigits

Expand Down

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