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XDS_from_H5.py
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#!/usr/bin/python
# -*- coding: utf-8 -*-
import sys
# Path needs to be be set only if dectris.albula is not found
# i.e. if ALBULA was installed without "--python=</path/to/python_interpreter>"
# Define correct path to ALBULA API:
try:
import albula as dec
except ImportError:
print("\nThe DECTRIS ALBULA API could not be loaded.")
print("If you did not install ALBULA with \"--python=</path/to/python_interpreter>\",")
print("please modify the \'sys.path.insert\' line in the script to point")
print("to the DECTRIS ALBULA API and uncomment the line.")
raise SystemExit
import os.path
import re
# This script was developed by Andreas Förster at DECTRIS based on work by Marcus Mueller.
# Please note that this is not an official DECTRIS product and neither endorsed nor supported by DECTRIS.
# Please report errors and problems to [email protected].
XDS_header_lines = """!*****************************************************************************
!
! XDS.INP template for ! %(family)s %(detector)s with %(sensor).2f mm thick silicon sensors.
!
! Characters to the right of an exclamation mark are comments.
!
! This file was autogenerated by XDS_from_H5.py (Oct 2015).
! Please check default values before processing.
!
! For questions and comments please contact [email protected].
!
!*****************************************************************************
"""
XDS_detector_lines = """
!====================== DETECTOR PARAMETERS ==================================
DETECTOR=%(family)s
MINIMUM_VALID_PIXEL_VALUE=0
OVERLOAD= %(cutoff)i ! taken from HDF5 header item
! /entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff
SENSOR_THICKNESS=%(sensor).2f ! [mm]
!SILICON=-1.0
QX=%(pixsize_x).3f QY=%(pixsize_y).3f ! [mm]
"""
XDS_main_lines = """
TRUSTED_REGION=0.0 1.41 !Relative radii limiting trusted detector region
DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 ! 0.0 cos(2theta) sin(2theta)
!====================== JOB CONTROL PARAMETERS ===============================
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
!JOB= DEFPIX INTEGRATE CORRECT
! MAXIMUM_NUMBER_OF_JOBS= 6 !Speeds up COLSPOT & INTEGRATE on multicore machine
! MAXIMUM_NUMBER_OF_PROCESSORS= 12 !<32;ignored by single cpu version of xds
!SECONDS=0 !Maximum number of seconds to wait until data image must appear
!TEST=1 !Test flag. 1,2 additional diagnostics and images
!====================== GEOMETRICAL PARAMETERS ===============================
!ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2
ORGX= %(orgx).1f ORGY= %(orgy).1f !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2
DETECTOR_DISTANCE= %(dist).2f ! [mm]
ROTATION_AXIS= 1.0 0.0 0.0
! Optimal choice is 0.5*mosaicity (REFLECTING_RANGE_E.S.D.= mosaicity)
OSCILLATION_RANGE=%(osc_range).5f ! [deg] (>0)
X-RAY_WAVELENGTH=%(wavelength).4f ! [A]
INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
FRACTION_OF_POLARIZATION=0.99 !default=0.5 for unpolarized beam
POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0
!======================= CRYSTAL PARAMETERS =================================
SPACE_GROUP_NUMBER=0 !0 for unknown crystals; cell constants are ignored.
UNIT_CELL_CONSTANTS= 0 0 0 0 0 0
! You may specify here the x,y,z components for the unit cell vectors if
! known from a previous run using the same crystal in the same orientation
!UNIT_CELL_A-AXIS=
!UNIT_CELL_B-AXIS=
!UNIT_CELL_C-AXIS=
!Optional reindexing transformation to apply on reflection indices
!REIDX= 0 0 -1 0 0 -1 0 0 -1 0 0 0
FRIEDEL'S_LAW= TRUE ! Default is TRUE.
!REFERENCE_DATA_SET= CK.HKL ! Name of a reference data set (optional)
!==================== SELECTION OF DATA IMAGES ==============================
!Generic file name and format (optional) of data images
NAME_TEMPLATE_OF_DATA_FRAMES=%(name_template)s ! HDF5
"""
XDS_tail_lines = """
!==================== DATA COLLECTION STRATEGY (XPLAN) ======================
! !!! Warning !!!
! If you processed your data for a crystal with unknown cell constants and
! space group symmetry, XPLAN will report the results for space group P1.
!STARTING_ANGLE= 0.0 STARTING_FRAME=1
!used to define the angular origin about the rotation axis.
!Default: STARTING_ANGLE= 0 at STARTING_FRAME=first data image
!RESOLUTION_SHELLS=10 6 5 4 3 2 1.5 1.3 1.2
!STARTING_ANGLES_OF_SPINDLE_ROTATION= 0 180 10
!TOTAL_SPINDLE_ROTATION_RANGES=30.0 120 15
!====================== INDEXING PARAMETERS =================================
!Never forget to check this, since the default 0 0 0 is almost always correct!
!INDEX_ORIGIN= 0 0 0 ! used by "IDXREF" to add an index offset
!Additional parameters for fine tuning that rarely need to be changed
!INDEX_ERROR=0.05 INDEX_MAGNITUDE=8 INDEX_QUALITY=0.8
SEPMIN=4.0 ! default is 6 for other detectors
CLUSTER_RADIUS=2 ! default is 3 for other detectors
!MAXIMUM_ERROR_OF_SPOT_POSITION=3.0
!MAXIMUM_ERROR_OF_SPINDLE_POSITION=2.0
!MINIMUM_FRACTION_OF_INDEXED_SPOTS=0.5
!============== DECISION CONSTANTS FOR FINDING CRYSTAL SYMMETRY =============
!Decision constants for detection of lattice symmetry (IDXREF, CORRECT)
MAX_CELL_AXIS_ERROR= 0.03 ! Maximum relative error in cell axes tolerated
MAX_CELL_ANGLE_ERROR= 2.0 ! Maximum cell angle error tolerated
!Decision constants for detection of space group symmetry (CORRECT).
!Resolution range for accepting reflections for space group determination in
!the CORRECT step. It should cover a sufficient number of strong reflections.
TEST_RESOLUTION_RANGE= 8.0 4.5
MIN_RFL_Rmeas= 50 ! Minimum #reflections needed for calculation of Rmeas
MAX_FAC_Rmeas= 2.0 ! Sets an upper limit for acceptable Rmeas
!================= PARAMETERS CONTROLLING REFINEMENTS =======================
REFINE(IDXREF)= BEAM AXIS ORIENTATION CELL ! POSITION
REFINE(INTEGRATE)= POSITION ORIENTATION ! BEAM CELL AXIS
REFINE(CORRECT)= POSITION BEAM ORIENTATION CELL AXIS
!================== CRITERIA FOR ACCEPTING REFLECTIONS ======================
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000 !Used by DEFPIX
!for excluding shaded parts of the detector.
INCLUDE_RESOLUTION_RANGE= 65.0 %(reso_range).1f !Angstroem; used by DEFPIX,INTEGRATE,CORRECT
!used by CORRECT to exclude ice-reflections
!EXCLUDE_RESOLUTION_RANGE= 3.93 3.87 !ice-ring at 3.897 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 3.70 3.64 !ice-ring at 3.669 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 3.47 3.41 !ice-ring at 3.441 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 2.70 2.64 !ice-ring at 2.671 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 2.28 2.22 !ice-ring at 2.249 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 2.102 2.042 !ice-ring at 2.072 Angstrom - strong
!EXCLUDE_RESOLUTION_RANGE= 1.978 1.918 !ice-ring at 1.948 Angstrom - weak
!EXCLUDE_RESOLUTION_RANGE= 1.948 1.888 !ice-ring at 1.918 Angstrom - strong
!EXCLUDE_RESOLUTION_RANGE= 1.913 1.853 !ice-ring at 1.883 Angstrom - weak
!EXCLUDE_RESOLUTION_RANGE= 1.751 1.691 !ice-ring at 1.721 Angstrom - weak
!MINIMUM_ZETA=0.05 !Defines width of 'blind region' (XPLAN,INTEGRATE,CORRECT)
!WFAC1=1.0 !This controls the number of rejected MISFITS in CORRECT;
!a larger value leads to fewer rejections.
!REJECT_ALIEN=20.0 ! Automatic rejection of very strong reflections
!============== INTEGRATION AND PEAK PROFILE PARAMETERS =====================
!Specification of the peak profile parameters below overrides the automatic
!determination from the images
!Suggested values are listed near the end of INTEGRATE.LP
!BEAM_DIVERGENCE= 0.80 !arctan(spot diameter/DETECTOR_DISTANCE)
!BEAM_DIVERGENCE_E.S.D.= 0.080 !half-width (Sigma) of BEAM_DIVERGENCE
!REFLECTING_RANGE= 0.780 !for crossing the Ewald sphere on shortest route
!REFLECTING_RANGE_E.S.D.= 0.113 !half-width (mosaicity) of REFLECTING_RANGE
! NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=15!used by: INTEGRATE
! NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=15 !used by: INTEGRATE
!DELPHI= 6.0!controls the number of reference profiles and scaling factors
!CUT=2.0 !defines the integration region for profile fitting
!MINPK=75.0 !minimum required percentage of observed reflection intensity
!======= PARAMETERS CONTROLLING CORRECTION FACTORS (used by: CORRECT) =======
!MINIMUM_I/SIGMA=3.0 !minimum intensity/sigma required for scaling reflections
!NBATCH=-1 !controls the number of correction factors along image numbers
!REFLECTIONS/CORRECTION_FACTOR=50 !minimum #reflections/correction needed
!PATCH_SHUTTER_PROBLEM=TRUE !FALSE is default
!STRICT_ABSORPTION_CORRECTION=TRUE !FALSE is default
!CORRECTIONS= DECAY MODULATION ABSORPTION
!=========== PARAMETERS DEFINING BACKGROUND AND PEAK PIXELS =================
!STRONG_PIXEL=3.0 !used by: COLSPOT
!A 'strong' pixel to be included in a spot must exceed the background
!by more than the given multiple of standard deviations.
!MAXIMUM_NUMBER_OF_STRONG_PIXELS=1500000 !used by: COLSPOT
!SPOT_MAXIMUM-CENTROID=3.0 !used by: COLSPOT
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 !used by: COLSPOT
!This allows to suppress spurious isolated pixels from entering the
!spot list generated by "COLSPOT".
!NBX=3 NBY=3 !Define a rectangle of size (2*NBX+1)*(2*NBY+1)
!The variation of counts within the rectangle centered at each image pixel
!is used for distinguishing between background and spot pixels.
!BACKGROUND_PIXEL=6.0 !used by: COLSPOT,INTEGRATE
!An image pixel does not belong to the background region if the local
!pixel variation exceeds the expected variation by the given number of
!standard deviations.
!SIGNAL_PIXEL=3.0 !used by: INTEGRATE
!A pixel above the threshold contributes to the spot centroid
!FIXED_SCALE_FACTOR=TRUE !Default is FALSE; used by : INIT,INTEGRATE
"""
detector_families = {
'pilatus' : {
'nmodules' : {
'12M': (5, 24),
'6M' : (5, 12),
'2M' : (3 ,8),
'1M' : (2, 5),
'300K-W': (3, 1),
'300K' : (1 ,3),
'200K' : (1 ,2),
'100K' : (1, 1),
},
'module' : {
'size': (487, 195),
'gap': (7, 17),
'pixel_size': (0.172e-03, 0.172e-03),
'nchips': (8, 2),
},
'chip': {
'size': (60, 97),
'gap': (1, 1),
},
'sizes' : {}, # will be populated with correct sizes
},
'eiger' : {
'nmodules' : {
'1M': (1, 2),
'4M': (2, 4),
'9M': (3, 6),
'16M': (4, 8),
},
'module' : {
'size': (1030, 514),
'gap': (10, 37),
'pixel_size': (0.075e-03, 0.075e-03),
'nchips': (4, 2),
},
'chip' : {
'size' : (256, 256),
'gap' : (2, 2),
},
'sizes' : {}, # will be populated with correct sizes
},
}
# All interesting parameters
incident_wavelength = "/entry/instrument/beam/incident_wavelength"
software_version = "/entry/instrument/detector/detectorSpecific/software_version"
beam_center_x = "/entry/instrument/detector/beam_center_x"
beam_center_y = "/entry/instrument/detector/beam_center_y"
x_pixel_size = "/entry/instrument/detector/x_pixel_size"
y_pixel_size = "/entry/instrument/detector/y_pixel_size"
detector_distance = "/entry/instrument/detector/detector_distance"
sensor_thickness = "/entry/instrument/detector/sensor_thickness"
nimages = "/entry/instrument/detector/detectorSpecific/nimages"
description = "/entry/instrument/detector/description"
omega_range_average = "/entry/sample/goniometer/omega_range_average"
omega_increment = "/entry/sample/goniometer/omega_increment"
countrate_correction_count_cutoff = "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff"
resolution_cutoff = 'max resolution'
# The list below contains the parameters to be extracted from H5
parameters = [
incident_wavelength,
software_version,
beam_center_x,
beam_center_y,
x_pixel_size,
y_pixel_size,
detector_distance,
sensor_thickness,
nimages,
description,
omega_range_average,
countrate_correction_count_cutoff,
resolution_cutoff
]
def create_XDS_INP(parameters, file_name):
lines = []
description = parameters["/entry/instrument/detector/description"].split()
family = description[1].lower()
sensor = float(parameters["/entry/instrument/detector/sensor_thickness"]) * 1000.0
FAMILY = family.upper()
det_name = description[2]
file_template = re.sub("master\.h5", "??????.h5", file_name)
lines.append(XDS_header_lines % {
'family': FAMILY,
'detector': det_name,
'sensor': sensor,})
lines.append(XDS_detector_lines % {
'family': FAMILY,
'cutoff': int(float(parameters["/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff"])),
'sensor': sensor,
'pixsize_x': float(parameters["/entry/instrument/detector/x_pixel_size"]) * 1000.0,
'pixsize_y': float(parameters["/entry/instrument/detector/y_pixel_size"]) * 1000.0,})
lines = lines + get_size_specific_lines(fam=family, det=det_name, n_excluded_edge_pixels=0)
lines.append(XDS_main_lines % {
'orgx': float(parameters["/entry/instrument/detector/beam_center_x"]),
'orgy': float(parameters["/entry/instrument/detector/beam_center_y"]),
'dist': float(parameters["/entry/instrument/detector/detector_distance"]) * 1000.0,
'osc_range': float(parameters["/entry/sample/goniometer/omega_range_average"]),
'wavelength': float(parameters["/entry/instrument/beam/incident_wavelength"]),
'name_template': file_template,})
first = 1
last = int(parameters["/entry/instrument/detector/detectorSpecific/nimages"])
para_images = int(full_parameters["/entry/instrument/detector/detectorSpecific/nimages"])
rotation = float(full_parameters["/entry/sample/goniometer/omega_range_average"])
lines.append("\n DATA_RANGE=%i %i\n" % (first, last))
if (para_images * rotation <= 30):
if (last > 100):
bkg = 100
else:
bkg = last
lines.append("\n")
lines.append(" BACKGROUND_RANGE=%i %i ! Numbers of first and last data image for background\n" % (first, bkg))
lines.append("!Five degrees are sufficient\n")
lines.append("\n")
lines.append(" SPOT_RANGE= %i %i ! Image range for finding spots\n" % (first, last))
lines.append("!Use all images if this range is not sufficient\n")
elif (para_images * rotation > 30):
# split spot finding into three 10 degree segments
bkg = first + int(5/rotation)
end1 = first + int(10/rotation)
start2 = first + int(last/2)
end2 = first + int(last/2) + int(10/rotation)
start3 = first + last - int(10/rotation) - 1
end3 = first + last - 1
lines.append("\n")
lines.append(" BACKGROUND_RANGE=%i %i ! Numbers of first and last data image for background\n" % (first, bkg))
lines.append("!Five degrees are sufficient\n")
lines.append("\n")
lines.append(" SPOT_RANGE= %i %i ! First image range for finding spots\n" % (first, end1))
lines.append(" SPOT_RANGE= %i %i ! Second image range for finding spots\n" % (start2, end2))
lines.append(" SPOT_RANGE= %i %i ! Third image range for finding spots\n" % (start3, end3))
lines.append("!Use all images if three ranges are not sufficient\n")
lines.append(XDS_tail_lines % {
'reso_range': float(parameters["max resolution"]),})
return lines
def get_size_specific_lines(fam, det, n_excluded_edge_pixels=0):
param_lines = []
gaps = calculate_gaps(
detector_families[fam]['sizes'][det],
detector_families[fam]['module']['size'],
detector_families[fam]['module']['gap'],
)
param_lines.append(' NX= %4d NY= %4d \n\n' % detector_families[fam]['sizes'][det])
param_lines.append('!EXCLUSION OF VERTICAL DEAD AREAS OF THE '
'%s %s DETECTOR \n' % (fam.upper(), det))
module_edge_comment = ('!EXCLUDING %d ADDITIONAL PIXELS OF THE '
'MODULE EDGES \n' % n_excluded_edge_pixels)
if n_excluded_edge_pixels > 0:
param_lines.append(module_edge_comment)
# offset is required because XDS.INP pixel values start with 1, not 0
offset = 1
for gap in gaps[0]:
param_lines.append(' UNTRUSTED_RECTANGLE= %4d %4d %4d %4d \n' % (
gap[0] - 1 + offset - n_excluded_edge_pixels,
gap[1] + 1 + offset + n_excluded_edge_pixels,
0,
detector_families[fam]['sizes'][det][1] + offset))
param_lines.append('\n')
param_lines.append('!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE '
'%s %s DETECTOR \n' % (fam.upper(), det))
if n_excluded_edge_pixels > 0:
param_lines.append(module_edge_comment)
for gap in gaps[1]:
param_lines.append(' UNTRUSTED_RECTANGLE= %4d %4d %4d %4d \n' % (
0,
detector_families[fam]['sizes'][det][0] + offset,
gap[0] - 1 + offset - n_excluded_edge_pixels,
gap[1] + 1 + offset + n_excluded_edge_pixels))
return param_lines
def warning():
return ('\nThis script extracts from a given HDF5 master file all metadata\n'
'required to write XDS.INP. The user is prompted for missing metadata.\n'
'\n'
'WARNING - This script is a proof-of-principle, pre-alpha.\n'
'Do not rely on it for anything serious. Things will go wrong.\n'
'In particular, this does not work for data collected in ROI mode.\n'
'\n'
'Please report shortcomings and errors to [email protected]\n')
def help():
return ('ERROR - You must specify exactly one HDF5 master file:\n'
'\n'
'python XDS_from_H5.py <name>_master.h5\n')
permitted_versions = ["1.6.2", "1.6.1", "1.6.0", "1.5.2", "1.5.1", "1.5.0", "1.2.0", "1.2.1", "1.3", "1.3.0", "1.4.0"]
def version_check(version):
if (str(version) in permitted_versions):
return 1
else:
return 0
zero_values = [0, "0", 0.0, "0.0"]
def isFile(file_input):
'''This function verifies that the file name entered by the user
corresponds to a master.h5 file and attaches an extension if necessary.'''
if os.path.isfile(file_input) and re.search("master\.h5\Z", file_input):
return file_input
elif os.path.isfile(file_input + ".h5") and re.search("master\Z", file_input):
return(file_input + ".h5")
else:
return 0
def request_parameter(parameter):
if (parameter == omega_range_average):
return raw_input("Please enter the oscillation range in degrees.\n")
elif (parameter == detector_distance):
return raw_input("Please enter the detector distance in meters.\n")
elif (parameter == incident_wavelength):
return raw_input("Please enter the wavelength in Angstrom.\n")
elif (parameter == beam_center_x):
return raw_input("Please enter the x coordinate of the beam center in pixels.\n")
elif (parameter == beam_center_y):
return raw_input("Please enter the y coordinate of the beam center in pixels.\n")
elif (parameter == x_pixel_size):
return raw_input("Please enter the x coordinate of the pixel size.\n")
elif (parameter == y_pixel_size):
return raw_input("Please enter the y coordinate of the pixel size.\n")
elif (parameter == sensor_thickness):
return raw_input("Please enter the sensor thickness in meters.\n")
elif (parameter == nimages):
return raw_input("Please enter the number of images.\n")
elif (parameter == description):
print("Please enter the description of the detector, e.g.")
return raw_input("Dectris Eiger 4M\n")
elif (parameter == countrate_correction_count_cutoff):
return raw_input("Please enter the maximum trusted pixel value.\n")
elif (parameter == resolution_cutoff):
#return raw_input("Please enter a resolution limit for processing.\n")
return 0
else:
print("Unknown software version. Please check.")
return 0
def calculate_gaps(det_size, mod_size, gap_size):
"""
Return list of tuples with first and last pixel in each detector gap.
One list for each detector dimension (x and y).
Input: total detector size in pixels
size of a module in pixels
size of a gap in pixels
"""
ndims = len(det_size)
gaps = []
for dim_index in range(ndims):
gaps.append([])
module_start = 0
while module_start < det_size[dim_index]:
# First pixel on a module has index 0, Python and C style
gap_start = module_start + mod_size[dim_index]
module_start = gap_start + gap_size[dim_index]
gap_end = module_start - 1
if module_start < det_size[dim_index]:
gaps[dim_index].append((gap_start, gap_end))
else:
break
return gaps
# Creates a dictionary of all keys and values in the NeXus tree
def iterate_children(node, nodeDict={}):
""" iterate over the children of a neXus node """
if node.type() == dec.DNeXusNode.GROUP:
for kid in node.children():
nodeDict = iterate_children(kid, nodeDict)
else:
nodeDict[node.path()] = node.value()
return nodeDict
# Extracts values from HDF5 file according to parameters array
def get_params(hdf5_file):
extracted = {}
h5cont = dec.DImageSeries(hdf5_file)
neXus_tree = h5cont.neXus()
neXus_root = neXus_tree.root()
neXus_string_tree = iterate_children(neXus_root)
if (len(sys.argv) == 2):
print("Extracting metadata from " + hdf5_file)
print("Please modify XDS.INP if these numbers are incorrect.\n")
for i in parameters:
if (neXus_string_tree.has_key(i)):
extracted[i] = str(neXus_string_tree[i])
else:
extracted[i] = ""
return extracted
def calculate_size(n_modules, mod_size, gap_size):
n_gaps = [n - 1 for n in n_modules]
size = []
for nmod, ngap, nmodpix, ngappix in zip(n_modules, n_gaps, mod_size, gap_size):
size.append(nmod * nmodpix + ngap * ngappix)
return tuple(size)
# populate dicts with sizes of detectors in pixels
for family in detector_families.values():
for model, n_modules in family['nmodules'].items():
family['sizes'][model] = calculate_size(n_modules=n_modules,
mod_size=family['module']['size'],
gap_size=family['module']['gap'])
if __name__ == "__main__":
if len(sys.argv) == 2:
# Make sure that XDS.INP does not already exist
if os.path.isfile ("XDS.INP"):
print("\nERROR: XDS.INP exists already. Please rename and rerun script.")
else:
# test whether argument 1 is HDF5 file.
# attach ".h5" if necessary
clean_file = isFile(sys.argv[1])
if (clean_file):
print(warning())
full_parameters = get_params(clean_file)
for i, v in full_parameters.iteritems():
if (v in zero_values):
print(i + " = " + str(v) + " <== WARNING: Should this really be 0?")
full_parameters[i] = request_parameter(i)
print(i + " = " + str(full_parameters[i]))
elif (v == "NaN") or (v == ""):
print(i + " = " + v + " <== ERROR: undefined value.")
full_parameters[i] = request_parameter(i)
print(i + " = " + str(full_parameters[i]))
else:
print(i + " = " + str(v))
para_version = str(full_parameters[software_version])
if version_check(para_version):
param_lines = create_XDS_INP(full_parameters, clean_file)
open("XDS.INP", 'w').writelines(param_lines)
print("\nFile XDS.INP was created successfully.")
if (int(full_parameters["/entry/instrument/detector/detectorSpecific/nimages"]) == 1):
print("However, there's not much you can do with one image.\n")
else:
print("Please verify its contents before processing data.\n")
else:
print("\nThe HDF5 file was created with version %s of the detector firmware" % (para_version))
print("This script supports versions 1.5 and up.")
print("Please extract metadata with hdfview or h5dump.\n")
else:
print(help())
elif (len(sys.argv) == 3):
# This assumes the second argument is the rotation range
# The script will run non-interactively
# The master.h5 must be specified with its full name
# An existing XDS.INP will be overwritten
full_parameters = get_params(sys.argv[1])
full_parameters["omega_range_average"] = sys.argv[2]
param_lines = create_XDS_INP(full_parameters, sys.argv[1])
open("XDS.INP", 'w').writelines(param_lines)
else:
print(help())
exit(-1)