jf8m master from geom script
This commit is contained in:
Beale John Henry
494
geom_files/jf8m_cxigeom2nexus.py
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494
geom_files/jf8m_cxigeom2nexus.py
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from __future__ import absolute_import, division, print_function
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from six.moves import range
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import os
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import h5py
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import numpy as np
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from read_geom import read_geom
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from libtbx.phil import parse
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import six
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from libtbx.utils import Sorry
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import datetime
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from jungfrau import pad_stacked_format
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phil_scope = parse("""
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unassembled_file = None
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.type = path
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.help = hdf5 file used to read in image data.
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geom_file = None
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.type = path
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.help = geometry file to be read in for detector (.geom).
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output_file = None
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.type = path
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.help = output file path
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detector_distance = None
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.type = float
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.help = Detector distance
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wavelength = None
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.type = float
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.help = If not provided, try to find wavelength in unassembled file.
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beam_file = None
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.type = path
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.help = Overrides wavelength. Reads the pulse IDs in the provided file \
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to get a list of wavelengths for the master.
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include_spectra = False
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.type = bool
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.help = If true, 2D spectral data will be included in the master file, \
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as read from the beam_file.
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energy_offset = None
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.type = float
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.help = If set, add this offset (in eV) to the energy axis in the \
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spectra in the beam file and to the per-shot wavelength.
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mask_file = None
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.type = str
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.help = Path to file with external bad pixel mask.
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split_modules_into_asics = True
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.type = bool
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.help = Whether to split the 4x2 modules into indivdual asics \
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accounting for borders and gaps.
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trusted_range = None
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.type = floats(size=2)
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.help = Set the trusted range
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raw = False
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.type = bool
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.help = Whether the data being analyzed is raw data from the JF16M or has \
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been corrected and padded.
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unassembled_data_key = None
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.type = str
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.expert_level = 2
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.help = Override hdf5 key name in unassembled file
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spectral_data_key = None
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.type = str
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.expert_level = 2
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.help = Override beam hdf5 file key for spectral data
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pedestal_file = None
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.type = str
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.help = path to Jungfrau pedestal file
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gain_file = None
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.type = str
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.help = path to Jungfrau gain file
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raw_file = None
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.type = str
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.help = path to Jungfrau raw file
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recalculate_wavelength = False
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.type = bool
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.help = If True, the incident_wavelength is recalculated from the \
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spectrum. The original wavelength is saved as \
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incident_wavelength_fitted_spectrum_average.
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nexus_details {
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instrument_name = SwissFEL ARAMIS BEAMLINE ESC
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.type = str
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.help = Name of instrument
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instrument_short_name = Cristallina
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.type = str
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.help = short name for instrument, perhaps the acronym
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source_name = SwissFEL ARAMIS
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.type = str
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.help = Name of the neutron or x-ray storage ring/facility
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source_short_name = SwissFEL ARAMIS
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.type = str
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.help = short name for source, perhaps the acronym
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start_time = None
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.type = str
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.help = ISO 8601 time/date of the first data point collected in UTC, \
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using the Z suffix to avoid confusion with local time
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end_time = None
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.type = str
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.help = ISO 8601 time/date of the last data point collected in UTC, \
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using the Z suffix to avoid confusion with local time. \
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This field should only be filled when the value is accurately \
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observed. If the data collection aborts or otherwise prevents \
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accurate recording of the end_time, this field should be omitted
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end_time_estimated = None
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.type = str
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.help = ISO 8601 time/date of the last data point collected in UTC, \
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using the Z suffix to avoid confusion with local time. \
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This field may be filled with a value estimated before an \
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observed value is avilable.
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sample_name = None
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.type = str
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.help = Descriptive name of sample
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total_flux = None
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.type = float
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.help = flux incident on beam plane in photons per second
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}
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""")
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'''
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This script creates a master nexus file by taking in as input a) an hdf5 file and b) a .geom file
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The hd5f file is generated by the JF16M after processing the raw images and doing appropriate gain corrections
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The assumed parameters for the detector can be seen in the __init__ function and should be changed
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if they are modified at in the future
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'''
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class jf16m_cxigeom2nexus(object):
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def __init__(self, args):
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self.params_from_phil(args)
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if self.params.detector_distance == None:
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self.params.detector_distance = 100.0 # Set detector distance arbitrarily if nothing is provided
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self.hierarchy = read_geom(self.params.geom_file)
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self.n_quads = 4
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self.n_modules = 4
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def params_from_phil(self, args):
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user_phil = []
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for arg in args:
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if os.path.isfile(arg):
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user_phil.append(parse(file_name=arg))
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else:
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try:
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user_phil.append(parse(arg))
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except Exception as e:
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raise Sorry("Unrecognized argument: %s"%arg)
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self.params = phil_scope.fetch(sources=user_phil).extract()
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def _create_scalar(self, handle,path,dtype,value):
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dataset = handle.create_dataset(path, (),dtype=dtype)
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dataset[()] = value
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def create_vector(self,handle, name, value, **attributes):
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handle.create_dataset(name, (1,), data = [value], dtype='f')
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for key,attribute in six.iteritems(attributes):
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handle[name].attrs[key] = attribute
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def create_nexus_master_file(self):
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'''
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Hierarchical structure of master nexus file. Format information available here
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http://download.nexusformat.org/sphinx/classes/base_classes/NXdetector_module.html#nxdetector-module
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--> entry
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--> data
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--> definition (leaf)
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--> instrument
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--> sample
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'''
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output_file_name = self.params.output_file if self.params.output_file is not None else os.path.splitext(self.params.unassembled_file)[0]+'_master.h5'
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f = h5py.File(output_file_name, 'w')
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f.attrs['NX_class'] = 'NXroot'
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f.attrs['file_name'] = os.path.basename(output_file_name)
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f.attrs['file_time'] = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H:%M:%SZ")
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f.attrs['HDF5_Version'] = h5py.version.hdf5_version
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entry = f.create_group('entry')
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entry.attrs['NX_class'] = 'NXentry'
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if self.params.nexus_details.start_time: entry['start_time'] = self.params.nexus_details.start_time
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if self.params.nexus_details.end_time: entry['end_time'] = self.params.nexus_details.end_time
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if self.params.nexus_details.end_time_estimated: entry['end_time_estimated'] = self.params.nexus_details.end_time_estimated
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# --> definition
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self._create_scalar(entry, 'definition', 'S4', np.string_('NXmx'))
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# --> data
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data = entry.create_group('data')
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data.attrs['NX_class'] = 'NXdata'
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data_key = 'data'
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if self.params.unassembled_data_key:
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unassembled_data_key = self.params.unassembled_data_key
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else:
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if self.params.raw:
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unassembled_data_key = "data/JF17T16V01"
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else:
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unassembled_file = h5py.File(self.params.unassembled_file, "r")
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unassembled_data_key = "data"
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if not unassembled_file.get(unassembled_data_key):
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unassembled_data_key = "data/JF17T16V01"
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if not unassembled_file.get(unassembled_data_key):
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raise Sorry("couldn't find unassembled data in the indicated file")
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unassembled_file.close()
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data[data_key] = h5py.ExternalLink(self.params.unassembled_file, unassembled_data_key+"/data")
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if self.params.raw_file is not None:
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assert not self.params.raw
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with h5py.File(self.params.pedestal_file, "r") as pedh5:
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print("Padding raw pedestal data")
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mean_pedestal = [pad_stacked_format(raw) for raw in pedh5["gains"]]
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print("Padding raw pedestal RMS data")
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sigma_pedestal = [pad_stacked_format(raw) for raw in pedh5["gainsRMS"]]
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data.create_dataset("pedestal", data=mean_pedestal, dtype=np.float32)
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data.create_dataset('pedestalRMS', data=sigma_pedestal, dtype=np.float32)
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with h5py.File(self.params.gain_file, "r") as gainh5:
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print("Padding gains")
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gains = [pad_stacked_format(raw) for raw in gainh5["gains"]]
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data.create_dataset("gains", data=gains, dtype=np.float32)
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data.attrs['signal'] = 'data'
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raw_file_handle = h5py.File(self.params.raw_file, "r")
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res_file_handle = h5py.File(self.params.unassembled_file, "r")
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raw_dset = raw_file_handle["data/JF17T16V01/data"]
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raw_shape = raw_dset.shape
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_, raw_slowDim, raw_fastDim = raw_shape
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raw_type = raw_dset.dtype
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num_imgs = res_file_handle['data/data'].shape[0]
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raw_layout = h5py.VirtualLayout(shape=(num_imgs, raw_slowDim, raw_fastDim), dtype=raw_type)
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raw_pulses = raw_file_handle['data/JF17T16V01/pulse_id'][()][:, 0]
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assert np.all(raw_pulses == np.sort(raw_pulses)) # NOTE; this is quick, however I think this is always the case
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res_pulses = h5py.File(self.params.unassembled_file, 'r')['data/pulse_id'][()]
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raw_source = h5py.VirtualSource(self.params.raw_file, 'data/JF17T16V01/data', shape=raw_shape)
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for res_imgnum, raw_imgnum in enumerate(np.searchsorted(raw_pulses, res_pulses)):
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raw_layout[res_imgnum] = raw_source[raw_imgnum]
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data.create_virtual_dataset('raw', raw_layout)
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if self.params.raw:
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if self.params.pedestal_file:
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# named gains instead of pedestal in JF data files
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data['pedestal'] = h5py.ExternalLink(self.params.pedestal_file, 'gains')
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data['pedestalRMS'] = h5py.ExternalLink(self.params.pedestal_file, 'gainsRMS')
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if self.params.gain_file:
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data['gains'] = h5py.ExternalLink(self.params.gain_file, 'gains')
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if self.params.pedestal_file or self.params.gain_file:
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data.attrs['signal'] = 'data'
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#--> sample
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sample = entry.create_group('sample')
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sample.attrs['NX_class'] = 'NXsample'
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if self.params.nexus_details.sample_name: sample['name'] = self.params.nexus_details.sample_name
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sample['depends_on'] = '.' # This script does not support scans/gonios
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# --> source
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source = entry.create_group('source')
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source.attrs['NX_class'] = 'NXsource'
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source['name'] = self.params.nexus_details.source_name
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source['name'].attrs['short_name'] = self.params.nexus_details.source_short_name
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# --> instrument
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instrument = entry.create_group('instrument')
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instrument.attrs['NX_class'] = 'NXinstrument'
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instrument["name"] = self.params.nexus_details.instrument_name
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instrument["name"].attrs["short_name"] = self.params.nexus_details.instrument_short_name
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beam = instrument.create_group('beam')
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beam.attrs['NX_class'] = 'NXbeam'
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if self.params.nexus_details.total_flux:
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self._create_scalar(beam, 'total_flux', 'f', self.params.nexus_details.total_flux)
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beam['total_flux'].attrs['units'] = 'Hz'
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if self.params.wavelength is None and self.params.beam_file is None:
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wavelengths = h5py.File(self.params.unassembled_file, 'r')['instrument/photon_wavelength_A']
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beam.create_dataset('incident_wavelength', (1,), data=np.mean(wavelengths), dtype='f8')
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elif self.params.beam_file is not None:
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# data file has pulse ids, need to match those to the beam file, which may have more pulses
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if self.params.raw:
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data_pulse_ids = h5py.File(self.params.unassembled_file, 'r')[unassembled_data_key+'/pulse_id'][()]
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else:
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data_pulse_ids = h5py.File(self.params.unassembled_file, 'r')[unassembled_data_key+'/pulse_id'][()]
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beam_h5 = h5py.File(self.params.beam_file, 'r')
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if self.params.spectral_data_key:
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spectral_data_key = self.params.spectral_data_key
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else:
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spectral_data_key = "SARFE10-PSSS059"
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if not beam_h5.get(spectral_data_key+":SPECTRUM_CENTER/pulse_id"):
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spectral_data_key = "data/SARFE10-PSSS059"
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if not beam_h5.get(spectral_data_key+":SPECTRUM_CENTER/pulse_id"):
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raise Sorry("couldn't find spectral data at the indicated address")
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beam_pulse_ids = beam_h5[spectral_data_key+':SPECTRUM_CENTER/pulse_id'][()]
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beam_energies = beam_h5[spectral_data_key+':SPECTRUM_CENTER/data'][()]
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energies = np.ndarray((len(data_pulse_ids),), dtype='f8')
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if self.params.recalculate_wavelength:
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orig_energies = np.ndarray((len(data_pulse_ids),), dtype='f8')
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if self.params.include_spectra:
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beam_spectra_x = beam_h5[spectral_data_key+':SPECTRUM_X/data'][()]
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beam_spectra_y = beam_h5[spectral_data_key+':SPECTRUM_Y/data'][()]
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spectra_x = np.ndarray((len(data_pulse_ids),beam_spectra_x.shape[1]), dtype='f8')
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spectra_y = np.ndarray((len(data_pulse_ids),beam_spectra_y.shape[1]), dtype='f8')
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for i, pulse_id in enumerate(data_pulse_ids):
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where = np.where(beam_pulse_ids==pulse_id)[0][0]
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if self.params.recalculate_wavelength:
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assert self.params.beam_file is not None, "Must provide beam file to recalculate wavelength"
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x = beam_spectra_x[where]
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y = beam_spectra_y[where].astype(float)
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ycorr = y - np.percentile(y, 10)
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e = sum(x*ycorr) / sum(ycorr)
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energies[i] = e
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orig_energies[i] = beam_energies[where]
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else:
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energies[i] = beam_energies[where]
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if self.params.include_spectra:
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spectra_x[i] = beam_spectra_x[where]
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spectra_y[i] = beam_spectra_y[where]
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if self.params.energy_offset:
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energies += self.params.energy_offset
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wavelengths = 12398.4187/energies
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if self.params.recalculate_wavelength:
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orig_wavelengths = 12398.4187/orig_energies
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beam.create_dataset('incident_wavelength', wavelengths.shape, data=wavelengths, dtype=wavelengths.dtype)
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if self.params.recalculate_wavelength:
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beam.create_dataset(
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'incident_wavelength_fitted_spectrum_average',
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orig_wavelengths.shape,
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data=orig_wavelengths,
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dtype=orig_wavelengths.dtype
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)
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beam['incident_wavelength_fitted_spectrum_average'].attrs['variant'] = 'incident_wavelength'
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if self.params.include_spectra:
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if self.params.energy_offset:
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spectra_x += self.params.energy_offset
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if (spectra_x == spectra_x[0]).all(): # check if all rows are the same
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spectra_x = spectra_x[0]
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beam.create_dataset('incident_wavelength_1Dspectrum', spectra_x.shape, data=12398.4187/spectra_x, dtype=spectra_x.dtype)
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beam.create_dataset('incident_wavelength_1Dspectrum_weight', spectra_y.shape, data=spectra_y, dtype=spectra_y.dtype)
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beam['incident_wavelength_1Dspectrum'].attrs['units'] = 'angstrom'
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beam['incident_wavelength'].attrs['variant'] = 'incident_wavelength_1Dspectrum'
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else:
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assert self.params.wavelength is not None, "Provide a wavelength"
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beam.create_dataset('incident_wavelength', (1,), data=self.params.wavelength, dtype='f8')
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beam['incident_wavelength'].attrs['units'] = 'angstrom'
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jf16m = instrument.create_group('JF8M')
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jf16m.attrs['NX_class'] = 'NXdetector_group'
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jf16m.create_dataset('group_index', data = list(range(1,3)), dtype='i')
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data = [np.string_('JF8M'),np.string_('ELE_D0')]
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jf16m.create_dataset('group_names',(2,), data=data, dtype='S12')
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jf16m.create_dataset('group_parent',(2,), data=[-1,1], dtype='i')
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jf16m.create_dataset('group_type', (2,), data=[1,2], dtype='i')
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detector = instrument.create_group('ELE_D0')
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detector.attrs['NX_class'] = 'NXdetector'
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detector['description'] = 'JUNGFRAU 8M'
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detector['depends_on'] = '/entry/instrument/ELE_D0/transformations/AXIS_RAIL'
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detector['gain_setting'] = 'auto'
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detector['sensor_material'] = 'Si'
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self._create_scalar(detector, 'sensor_thickness', 'f', 320.)
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self._create_scalar(detector, 'bit_depth_readout', 'i', 16)
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self._create_scalar(detector, 'count_time', 'f', 10)
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self._create_scalar(detector, 'frame_time', 'f', 40)
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detector['sensor_thickness'].attrs['units'] = 'microns'
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detector['count_time'].attrs['units'] = 'us'
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detector['frame_time'].attrs['units'] = 'us'
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transformations = detector.create_group('transformations')
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transformations.attrs['NX_class'] = 'NXtransformations'
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# Create AXIS leaves for RAIL, D0 and different hierarchical levels of detector
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self.create_vector(transformations, 'AXIS_RAIL', self.params.detector_distance, depends_on='.', equipment='detector', equipment_component='detector_arm',transformation_type='translation', units='mm', vector=(0., 0., 1.), offset=(0.,0.,0.))
|
||||
self.create_vector(transformations, 'AXIS_D0', 0.0, depends_on='AXIS_RAIL', equipment='detector', equipment_component='detector_arm',transformation_type='rotation', units='degrees', vector=(0., 0., -1.), offset=self.hierarchy.local_origin, offset_units = 'mm')
|
||||
# Add 4 quadrants
|
||||
# Nexus coordiate system, into the board JF16M detector
|
||||
# o --------> (+x) Q3=(12,13,14,15) Q0=(0,1,2,3)
|
||||
# | o
|
||||
# | Q2=(8,9,10,11) Q1=(4,5,6,7)
|
||||
# v
|
||||
# (+y)
|
||||
|
||||
panels = []
|
||||
for q, quad in six.iteritems(self.hierarchy):
|
||||
panels.extend([quad[key] for key in quad])
|
||||
pixel_size = panels[0]['pixel_size']
|
||||
assert [pixel_size == panels[i+1]['pixel_size'] for i in range(len(panels)-1)].count(False) == 0
|
||||
if self.params.raw:
|
||||
fast = 1030; slow = 8224
|
||||
else:
|
||||
fast = max([int(panel['max_fs']) for panel in panels])+1
|
||||
slow = max([int(panel['max_ss']) for panel in panels])+1
|
||||
|
||||
quad_fast = fast
|
||||
quad_slow = slow // self.n_quads
|
||||
module_fast = quad_fast
|
||||
module_slow = quad_slow // self.n_modules
|
||||
|
||||
if self.params.split_modules_into_asics:
|
||||
n_fast_asics = 4; n_slow_asics = 2
|
||||
if self.params.raw:
|
||||
border = 1; data_gap = 0; real_gap = 2
|
||||
asic_fast = (module_fast - (n_fast_asics-1)*data_gap) / n_fast_asics # includes border but not gap
|
||||
asic_slow = (module_slow - (n_slow_asics-1)*data_gap) / n_slow_asics # includes border but not gap
|
||||
else:
|
||||
border = 1; gap = 2
|
||||
asic_fast = (module_fast - (n_fast_asics-1)*gap) / n_fast_asics # includes border but not gap
|
||||
asic_slow = (module_slow - (n_slow_asics-1)*gap) / n_slow_asics # includes border but not gap
|
||||
|
||||
array_name = 'ARRAY_D0'
|
||||
|
||||
if self.params.mask_file is not None:
|
||||
self._create_scalar(detector, 'pixel_mask_applied', 'b', True)
|
||||
#detector['pixel_mask'] = h5py.ExternalLink(self.params.mask_file, "mask") # If mask was formatted right, could use this
|
||||
mask = h5py.File(self.params.mask_file, 'r')['pixel_mask'][()].astype(np.int32)
|
||||
detector.create_dataset('pixel_mask', mask.shape, data=mask==0, dtype=mask.dtype)
|
||||
|
||||
if self.params.trusted_range is not None:
|
||||
underload, overload = self.params.trusted_range
|
||||
detector.create_dataset('underload_value', (1,), data=[underload], dtype='int32')
|
||||
detector.create_dataset('saturation_value', (1,), data=[overload], dtype='int32')
|
||||
|
||||
alias = 'data'
|
||||
data_name = 'data'
|
||||
detector[alias] = h5py.SoftLink('/entry/data/%s'%data_name)
|
||||
|
||||
for q_key in sorted(self.hierarchy.keys()):
|
||||
quad = int(q_key.lstrip('quad'))
|
||||
q_name = 'AXIS_D0Q%d'%quad
|
||||
quad_vector = self.hierarchy[q_key].local_origin.elems
|
||||
self.create_vector(transformations, q_name, 0.0, depends_on='AXIS_D0', equipment='detector', equipment_component='detector_quad',transformation_type='rotation', units='degrees', vector=(0., 0., -1.), offset = quad_vector, offset_units = 'mm')
|
||||
for m_key in sorted(self.hierarchy[q_key].keys()):
|
||||
module_num = int(m_key.lstrip('m'))
|
||||
m_name = 'AXIS_D0Q%dM%d'%(quad, module_num)
|
||||
module_vector = self.hierarchy[q_key][m_key]['local_origin']
|
||||
fast = self.hierarchy[q_key][m_key]['local_fast']
|
||||
slow = self.hierarchy[q_key][m_key]['local_slow']
|
||||
if self.params.split_modules_into_asics:
|
||||
# module_vector points to the corner of the module. Instead, point to the center of it.
|
||||
offset = (module_fast/2 * pixel_size * fast) + (module_slow/2 * pixel_size * slow)
|
||||
module_vector = module_vector + offset
|
||||
self.create_vector(transformations, m_name, 0.0, depends_on=q_name, equipment='detector', equipment_component='detector_module',transformation_type='rotation', units='degrees', vector=(0., 0., -1.), offset = module_vector.elems, offset_units = 'mm')
|
||||
|
||||
for asic_fast_number in range(n_fast_asics):
|
||||
for asic_slow_number in range(n_slow_asics):
|
||||
asic_num = asic_fast_number + (asic_slow_number * n_fast_asics)
|
||||
a_name = 'AXIS_D0Q%dM%dA%d'%(quad, module_num, asic_num)
|
||||
# Modules look like this:
|
||||
# bbbbbggbbbbb Assuming a 3x3 asic (X), a 1 pixel border (b) and a 2 pixel gap (g).
|
||||
# bXXXbggbXXXb This is as if there were only two asics in a module
|
||||
# bXXXbggbXXXb The math below skips past the borders and gaps to the first real pixel.
|
||||
# bXXXbggbXXXb
|
||||
# bbbbbggbbbbb
|
||||
if self.params.raw:
|
||||
asic_vector = -offset + (fast * pixel_size * (asic_fast * asic_fast_number + border + (asic_fast_number * real_gap))) + \
|
||||
(slow * pixel_size * (asic_slow * asic_slow_number + border + (asic_slow_number * real_gap)))
|
||||
else:
|
||||
asic_vector = -offset + (fast * pixel_size * (asic_fast * asic_fast_number + border + (asic_fast_number * gap))) + \
|
||||
(slow * pixel_size * (asic_slow * asic_slow_number + border + (asic_slow_number * gap)))
|
||||
|
||||
self.create_vector(transformations, a_name, 0.0, depends_on=m_name, equipment='detector', equipment_component='detector_asic',
|
||||
transformation_type='rotation', units='degrees', vector=(0., 0., -1.), offset = asic_vector.elems, offset_units = 'mm')
|
||||
|
||||
asicmodule = detector.create_group(array_name+'Q%dM%dA%d'%(quad,module_num,asic_num))
|
||||
asicmodule.attrs['NX_class'] = 'NXdetector_module'
|
||||
if self.params.raw:
|
||||
asicmodule.create_dataset('data_origin', (2,), data=[module_slow * module_num + asic_slow * asic_slow_number + border + data_gap*asic_slow_number,
|
||||
asic_fast * asic_fast_number + border + data_gap*asic_fast_number], dtype='i')
|
||||
else:
|
||||
asicmodule.create_dataset('data_origin', (2,), data=[module_slow * module_num + asic_slow * asic_slow_number + border + gap*asic_slow_number,
|
||||
asic_fast * asic_fast_number + border + gap*asic_fast_number], dtype='i')
|
||||
asicmodule.create_dataset('data_size', (2,), data=[asic_slow - border*2, asic_fast - border*2], dtype='i')
|
||||
|
||||
self.create_vector(asicmodule, 'fast_pixel_direction',pixel_size,
|
||||
depends_on=transformations.name+'/AXIS_D0Q%dM%dA%d'%(quad,module_num,asic_num),
|
||||
transformation_type='translation', units='mm', vector=fast.elems, offset=(0. ,0., 0.))
|
||||
self.create_vector(asicmodule, 'slow_pixel_direction',pixel_size,
|
||||
depends_on=transformations.name+'/AXIS_D0Q%dM%dA%d'%(quad,module_num,asic_num),
|
||||
transformation_type='translation', units='mm', vector=slow.elems, offset=(0., 0., 0.))
|
||||
else:
|
||||
module_vector = self.hierarchy[q_key][m_key]['local_origin'].elems
|
||||
self.create_vector(transformations, m_name, 0.0, depends_on=q_name,
|
||||
equipment='detector', equipment_component='detector_module',
|
||||
transformation_type='rotation', units='degrees', vector=(0. ,0., -1.),
|
||||
offset = module_vector, offset_units = 'mm')
|
||||
|
||||
modulemodule = detector.create_group(array_name+'Q%dM%d'%(quad,module_num))
|
||||
modulemodule.attrs['NX_class'] = 'NXdetector_module'
|
||||
modulemodule.create_dataset('data_origin', (2,), data=[module_slow * module_num, 0],
|
||||
dtype='i')
|
||||
modulemodule.create_dataset('data_size', (2,), data=[module_slow, module_fast], dtype='i')
|
||||
|
||||
fast = self.hierarchy[q_key][m_key]['local_fast'].elems
|
||||
slow = self.hierarchy[q_key][m_key]['local_slow'].elems
|
||||
self.create_vector(modulemodule, 'fast_pixel_direction',pixel_size,
|
||||
depends_on=transformations.name+'/AXIS_D0Q%dM%d'%(quad,module_num),
|
||||
transformation_type='translation', units='mm', vector=fast, offset=(0. ,0., 0.))
|
||||
self.create_vector(modulemodule, 'slow_pixel_direction',pixel_size,
|
||||
depends_on=transformations.name+'/AXIS_D0Q%dM%d'%(quad,module_num),
|
||||
transformation_type='translation', units='mm', vector=slow, offset=(0., 0., 0.))
|
||||
f.close()
|
||||
|
||||
if __name__ == '__main__':
|
||||
import sys
|
||||
nexus_helper = jf16m_cxigeom2nexus(sys.argv[1:])
|
||||
nexus_helper.create_nexus_master_file()
|
||||
Reference in New Issue
Block a user