brkraw 0.3.11__py3-none-any.whl → 0.5.0__py3-none-any.whl

brkraw/lib/reference.py

@@ -1,245 +0,0 @@
-# REGEX patterns
-ptrn_param          = r'^\#\#(?P<key>.*)\=(?P<value>.*)$'
-ptrn_key            = r'^\$(?P<key>.*)'
-ptrn_array          = r"\((?P<array>[^()]*)\)"
-ptrn_complex_array  = r"\((?P<comparray>\(.*)\)$"
-ptrn_comment        = r'\$\$.*'
-ptrn_float          = r'^-?\d+\.\d+$'
-ptrn_engnotation    = r'^-?[0-9.]+e-?[0-9.]+$'
-ptrn_integer        = r'^[-]*\d+$'
-ptrn_string         = r'^\<(?P<string>[^>]*)\>$'
-ptrn_arraystring    = r'\<(?P<string>[^>]*)\>[,]*'
-ptrn_bisstring      = r'\<(?P<string>\$Bis[^>]*)\#\>'
-ptrn_braces         = r'\((?P<contents>[^()]*)\)'
-# [20210820] Add-paravision 360 related. @[number of repititions]([number]) ex) @5(0)
-ptrn_at_array       = r'@(\d*)\*\(([-]?\d*[.]?\d*[eE]?[-]?\d*?)\)'
-
-# Conditional variables
-HEADER = 0
-PARAMETER = 1
-
-# Parameters
-WORDTYPE = \
-    dict(_32BIT_SGN_INT     = 'i',
-         _16BIT_SGN_INT     = 'h',
-         _8BIT_UNSGN_INT    = 'B',
-         _32BIT_FLOAT       = 'f')
-BYTEORDER = \
-    dict(littleEndian       = '<',
-         bigEndian          = '>')
-
-SLICE_ORIENT = {0: {1: 'L->R', 3: 'R->L'},
-                1: {1: 'P->A', 3: 'A->P'},
-                2: {1: 'F->H', 3: 'F->H'},
-                }
-
-ISSUE_REPORT = 'Please report the issue at (https://github.com/dvm-shlee/bruker/issues) with the error message.'
-
-ERROR_MESSAGES = {'ImportError'         : '[{}] is not recognized as ParavisionDataset.',
-                  'NoSlicePacksDef'     : 'NoneType VisuCoreSlicePacksDef.',
-                  'SliceDistDatatype'   : 'unexpected datatype of VisuCoreSliceDist.',
-                  'SlicePacksSlices'    : 'unexpected datatype of VisuCoreSlicePacksSlices',
-                  'DimType'             : 'non compatible dimension type.',
-                  'NumOrientMatrix'     : 'unexpected number of element in VisuCoreOrientation.',
-                  'NumSlicePosition'    : 'unexpected number of element in VisuCorePosition.',
-                  'PhaseEncDir'         : 'unexpected phase encoding direction.',
-                  'NotIntegrated'       : 'not integrated method, please contact developer.'
-                  }
-
-# BIDS v1.2.2
-# Below is the list of METADATA keywords that BIDS recommended
-COMMON_METADATA_FIELD = \
-    dict(Recommended    = [  # SCANNER_HARDWARE
-                           'Manufacturer',
-                           'ManufacturersModelName',
-                           'DeviceSerialNumber',
-                           'StationName',
-                           'SoftwareVersion',
-                           'MagneticFieldStrength',
-                           'ReceiveCoilName',
-                           'ReceiveCoilActiveElements',
-                           'GradientSetType',
-                           'MRTransmitCoilSequence',
-                           'MatrixCoilMode',
-                           'CoilCombinationMethod',
-
-                             # SEQUENCE_SPECIFIC
-                           'PulseSequenceType',
-                           'ScanningSequence',
-                           'SequenceVariant',
-                           'ScanOptions',
-                           'SequenceName',
-                           'PulseSequenceDetails',
-                           'NonlinearGradientCorrection',
-
-                             # IN_PLANE_SPATIAL_ENCODING
-                           'NumberShots',
-                           'ParallelReductionFactorInPlane',
-                           'ParallelAcquisitionTechnique',
-                           'PartialFourier',
-                           'PartialFourierDirection',
-                           'PhaseEncodingDirection',
-                           'EffectiveEchoSpacing',
-                           'TotalReadoutTime',
-
-                             # TIMING_PARAMETERS
-                           'EchoTime',
-                           'InversionTime',
-                           'SliceTiming',
-                           'SliceEncodingDirection',
-                           'DwellTime',
-
-                             # RF_AND_CONTRAST, SLICE_ACCELERATION
-                           'FlipAngle',
-                           'MultibandAccerlationFactor',
-                           'AnatomicalLandmarkCoordinates',
-
-                             # INSTITUTION_INFORMATION
-                           'InstitutionName',
-                           'InstitutionAddress',
-                           'InstitutionalDepartmentName'],
-
-             Optional   = [  # RF_AND_CONTRAST
-                           'NegativeContrast',
-
-                             # ACQUISITION_SPECIFIC
-                           'ContrastBolusIngredient'],
-
-             Deprecated = [  # SCANNER_HARDWARE
-                           'HardcopyDeviceSoftwareVersion'])
-
-# Matadata Field Mapping for Bruker PvDataset
-# BIDS Meta data will be automatically created according to below reference.
-# If list is entered as value, each parameter will be tested and the first available value will be returned.
-# If dict is entered as value, below condition will be tested.
-#   If key - where pair:  parse value from given key and return index of 'where' from these values
-#   If key - idx pair:    parse value from given key and return value of given 'idx'
-#   If 'Equation' in key: each key assigned as local variable and test in Equation will be executed to return the value
-#   Else, new key - value dictionary will be return (for the cases with sub-keys)
-# If string is entered as value, The value of given parameter will be parsed from parameter files
-COMMON_META_REF = \
-    dict(Manufacturer                   = 'VisuManufacturer',
-         ManufacturersModelName         = 'VisuStation',
-         DeviceSerialNumber             = 'VisuSystemOrderNumber',
-         StationName                    = 'VisuStation',
-         SoftwareVersion                = 'VisuAcqSoftwareVersion',
-         MagneticFieldStrength          = dict(Freq     = 'VisuAcqImagingFrequency',
-                                               Equation = 'Freq / 42.576'),
-         ReceiveCoilName                = 'VisuCoilReceiveName',
-         ReceiveCoilActiveElements      = 'VisuCoilReceiveType',
-         GradientSetType                = 'ACQ_status',
-         MRTransmitCoilSequence         = dict(Name         = 'VisuCoilTransmitName',
-                                               Manufacture  = 'VisuCoilTransmitManufacturer',
-                                               Type         = 'VisuCoilTransmitType'),
-         CoilConfigName                 = 'ACQ_coil_config_file',  # if Transmit and Receive coil info in None
-         MatrixCoilMode                 = 'ACQ_experiment_mode',
-         CoilCombinationMethod          = None,
-
-         # SEQUENCE_SPECIFIC
-         PulseSequenceType              = 'PULPROG',  # 'VisuAcqEchoSequenceType'
-         ScanningSequence               = 'VisuAcqSequenceName',
-         SequenceVariant                = 'VisuAcqEchoSequenceType',
-         ScanOptions                    = dict(RG   = 'VisuRespSynchUsed',
-                                               CG   = 'VisuCardiacSynchUsed',
-                                               PFF  = dict(key = 'VisuAcqPartialFourier',
-                                                           idx = 0),
-                                               PFP  = dict(key = 'VisuAcqPartialFourier',
-                                                           idx = 1),
-                                               FC   = 'VisuAcqFlowCompensation',
-                                               SP   = 'PVM_FovSatOnOff',
-                                               FP   = 'VisuAcqSpectralSuppression'),
-         SequenceName                   = ['VisuAcquisitionProtocol',
-                                           'ACQ_protocol_name'],  # if first component are None
-         PulseSequenceDetails           = 'ACQ_scan_name',
-         NonlinearGradientCorrection    = 'VisuAcqKSpaceTraversal',
-
-         # IN_PLANE_SPATIAL_ENCODING
-         NumberShots                    = 'VisuAcqKSpaceTrajectoryCnt',
-         ParallelReductionFactorInPlane = 'ACQ_phase_factor',
-         ParallelAcquisitionTechnique   = None,
-         PartialFourier                 = 'VisuAcqPartialFourier',
-         PartialFourierDirection        = None,
-         PhaseEncodingDirection         = [dict(key         = 'VisuAcqGradEncoding',
-                                                where       = 'phase_enc'),
-                                           'VisuAcqImagePhaseEncDir'],  # Deprecated
-         EffectiveEchoSpacing           = dict(BWhzPixel    = 'VisuAcqPixelBandwidth',
-                                               MatSizePE    = dict(key='PVM_EncMatrix',
-                                                                   idx=[dict(key    = 'VisuAcqGradEncoding',
-                                                                             where  = 'phase_enc'),
-                                                                        1]),  # PV5.1
-                                               ACCfactor    = 'ACQ_phase_factor',
-                                               Equation     = '(1 / (MatSizePE * BWhzPixel)) / ACCfactor'),  # in second
-         TotalReadoutTime               = dict(ETL          = 'VisuAcqEchoTrainLength',
-                                               BWhzPixel    = 'VisuAcqPixelBandwidth',
-                                               ACCfactor    = 'ACQ_phase_factor',
-                                               Equation     = '(1 / BWhzPixel) / ACCfactor'),
-
-         # TIMING_PARAMETERS
-         EchoTime                       = dict(TE           = 'VisuAcqEchoTime',
-                                               Equation     = 'np.array(TE)/1000'),
-         InversionTime                  = 'VisuAcqInversionTime',
-         SliceTiming                    = dict(TR           = 'VisuAcqRepetitionTime',
-                                               Num_of_Slice = 'VisuCoreFrameCount',
-                                               Order        = 'ACQ_obj_order',
-                                               Equation     = 'np.linspace(0, TR/1000, Num_of_Slice + 1)[Order]'),
-         SliceEncodingDirection         = [dict(key         = 'VisuAcqGradEncoding',
-                                                where       = 'slice_enc'),
-                                           dict(EncSeq      = 'VisuAcqGradEncoding',
-                                                Equation    = 'len(EncSeq)')],
-         DwellTime                      = dict(BWhzPixel    ='VisuAcqPixelBandwidth',
-                                               Equation     ='1/BWhzPixel'),
-
-         # RF_AND_CONTRAST, SLICE_ACCELERATION
-         FlipAngle                      = 'VisuAcqFlipAngle',
-         MultibandAccerlationFactor     = None,
-         AnatomicalLandmarkCoordinates  = None,
-
-         # INSTITUTION_INFORMATION
-         InstitutionName                = 'VisuInstitution',
-         InstitutionAddress             = None,
-         InstitutionalDepartmentName    = None)
-
-
-FMRI_META_REF = \
-    dict(RepetitionTime                 = dict(TR           = 'VisuAcqRepetitionTime',
-                                               Equation     = 'TR/1000'),
-         VolumeTiming                   = dict(TR           = 'VisuAcqRepetitionTime',
-                                               NR           = 'PVM_NRepetitions',
-                                               Equation     = '(np.arange(NR)*(TR/1000)).tolist()'),
-         TaskName                       = None,
-
-         # RECOMMENDED
-         # - timing parameters
-         NumberOfVolumesDiscardedByScanner  = 'PVM_DummyScans',
-         NumberOfVolumesDiscardedByUser     = None,
-         DelayTime                      = None,
-         AcquisitionDuration            = dict(TR           = "PVM_ScanTime",
-                                               Equation     = "TR/1000"),
-         DelayAfterTrigger              = None,
-
-         # - fMRI task information
-         Instructions                   = None,
-         TaskDescription                = None,
-         CogAtlasID                     = 'https://www.cognitiveatlas.org/fillYourID',
-         CogPOID                        = 'http://www.cogpo.org/fillYourID'
-         )
-
-
-FIELDMAP_META_REF = \
-    dict(IntendedFor                    = '',
-         )
-
-DATASET_DESC_REF = \
-    dict(Name='',
-         BIDSVersion='1.2.2',
-         License='',
-         Authors=[''],
-         Acknowledgements='',
-         HowToAsknowledge='',
-         Funding=[''],
-         EthicApprovals='',
-         ReferenceAndLinks='',
-         DatasetDOI='')
-
-XYZT_UNITS = \
-    dict(EPI=('mm', 'sec'))