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Commit e95fbcb5 authored by Mo Shahdloo's avatar Mo Shahdloo
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Merge branch 'dev' of https://git.fmrib.ox.ac.uk/shahdloo/pymapvbvd 

Conflicts:
	requirements.txt
	tests/test_flags.py
	tests/test_svs.py
parents 6029b436 6307f3ef
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mapVBVD/_version.py export-subst
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include requirements.txt
include versioneer.py
include mapVBVD/_version.py
include LICENSE
README.md
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Python port of the Matlab mapVBVD tool for reading Siemens raw data .dat 'twix' files.
# pyMapVBVD
![PyPI](https://img.shields.io/pypi/v/pyMapVBVD)
![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyMapVBVD)
Python port of the Matlab mapVBVD tool for reading Siemens raw data 'twix' (.dat) files.
## Use
I have attempted to replicate the syntax of the original matlab code, but there are a few differences due to differing variable types.
This package contains a demo Jupyter notebook 'Demo.ipynb' which can be run on the two bits of demo data found in tests/test_data. Both of these data are unsuppressed water SVS MRS, one from a 7T VB scanner and the other from a VE Prisma.
Run using the following:
```
twixObj = mapVBVD(filename)
```
For multi raid files (VD+) twixObj is a list, for single files it is a dict containing data with keys relating to the evalinfo flags and a header object. `twixObj.keys()`
For multi raid files (VD+) twixObj is a list, for single files it is a AttrDict containing data with keys relating to the MDH flags and a header object. The MDH flags present can be retrieved as a list using `twixObj.MDH_flags()`, whilst the header is found at `twixObj.hdr`.
## Data
Data can be accessed using e.g.
Data can be accessed using e.g. for image MDH
```
data = twixObj[currKey]['']
data = twixObj[currKey][:,:,:]
data = twixObj[currKey][:,0,:]
data = twixObj.image['']
data = twixObj.image[:,:,:]
data = twixObj.image[0::2,0,:]
```
To remove singleton dimensions `twixObj['image'].squeeze = True`.
To remove singleton dimensions `twixObj.image.squeeze = True`.
To retrieve the data in an unsorted format (i.e. Col,Cha,NAcq) use `twixObj.image.unsorted()`.
## Headers
Header information is contained in a dict `twixObj.hdr`
`twixObj.hdr.keys()` provides a list of the data containers.
Access them manually using e.g. `twixObj.hdr['MeasYaps']` or `twixObj.hdr.MeasYaps`.
These objects are in turn a final level of dictionaries. The actual data values can be accessed either manually using tuples of key values e.g.
```
twixObj.hdr.MeasYaps[('sTXSPEC','asNucleusInfo','0','tNucleus')]
```
or you can search for keys and values by custom methods.
```
matching_keys = twixObj.search_header_for_keys(('sTXSPEC', 'asNucleusInfo'))
key_value = twixObj.search_header_for_val('MeasYaps',('sTXSPEC', 'asNucleusInfo', '0', 'tNucleus'))
```
Header information is contained in a dict `twixObj['hdr']`
`twixObj['hdr'].keys()` provides a list of the data containers.
Acess them using e.g. `twixObj['hdr']['MeasYaps']`
These objects are in turn a final level of dictionaries. The actual data values can be accessed using tuples of key values.
`search_header_for_keys` takes the keyword argument regex (default True) to either search via case insensitive regular expressions or via exact matches only. Specify top_lvl to restrict to just some parameter sets.
Much of the auxillery parts of mapVBVD (e.g. line reflection, OS removal) is not yet implemented. Please feel free to contribute these parts! As this is a port the code is intended to resemble the original matlab code, it is not "good" python code!
## Other info
Much of the auxiliary parts of mapVBVD (e.g. line reflection, OS removal) is not yet implemented. Please feel free to contribute these parts! As this is a port the code is intended to resemble the original matlab code, it is not "good" python code!
## Credit where credit is due
This code is a port of Philipp Ehses' original Matlab code. I am incredibly grateful to him for releasing this code to the MR community. There are a number of other names in the original code comments and log, these are: Felix Breuer, Wolf Blecher, Stephen Yutzy, Zhitao Li, Michael VÃlker, Jonas Bause and Chris Mirke.
This port is released under the MIT licence and no credit is sought for its use.
\ No newline at end of file
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import numpy as np
from dataclasses import dataclass, field
from read_twix_hdr import read_twix_hdr
from twix_map_obj import twix_map_obj
from tqdm import tqdm, trange
def bitget(number, pos):
return (number >> pos) & 1
def set_bit(v, index, x):
# Set the index:th bit of v to 1 if x is truthy, else to 0, and return the new value."""
mask = 1 << index # Compute mask, an integer with just bit 'index' set.
v &= mask # Clear the bit indicated by the mask (if x is False)
if x:
v |= mask # If x was True, set the bit indicated by the mask.
return v # Return the result, we're done.
def loop_mdh_read(fid, version, Nscans, scan, measOffset, measLength):
if version == 'vb':
isVD = False
byteMDH = 128
elif version == 'vd':
isVD = True
byteMDH = 184
szScanHeader = 192 # [bytes]
szChannelHeader = 32 # [bytes]
else:
isVD = False
byteMDH = 128
import warnings
warnings.warn(f'Software version "{version}" is not supported.')
cPos = fid.tell()
n_acq = 0
allocSize = 4096
ulDMALength = byteMDH
isEOF = False
mdh_blob = np.zeros((byteMDH, 0), dtype=np.uint8)
szBlob = mdh_blob.shape[1] # pylint: disable=E1136 # pylint/issues/3139
filePos = np.zeros((0), dtype=float)
fid.seek(cPos, 0)
# constants and conditional variables
bit_0 = np.array(2 ** 0, dtype=np.uint8)
bit_5 = np.array(2 ** 5, dtype=np.uint8)
mdhStart = -byteMDH # Different to matlab - index = -128
u8_000 = np.zeros((3, 1), dtype=np.uint8)
# 20 fill bytes in VD (21:40)
# Subtract one from Idx numbers to account for indexing from 0 in python
evIdx = np.array(21 + 20 * isVD, dtype=np.uint8) - 1 # 1st byte of evalInfoMask
dmaIdx = np.array(np.arange(29, 33) + 20 * isVD, dtype=np.uint8) - 1 # to correct DMA length using NCol and NCha
if isVD:
dmaOff = szScanHeader
dmaSkip = szChannelHeader
else:
dmaOff = 0
dmaSkip = byteMDH
t = tqdm(total=np.float(str('%8.1f' % (measLength/1024**2))), desc='Scan %d/%d, read all mdhs' % (scan + 1, Nscans), leave=True)
while True:
# Read mdh as binary (uint8) and evaluate as little as possible to know...
# ... where the next mdh is (ulDMALength / ushSamplesInScan & ushUsedChannels)
# ... whether it is only for sync (MDH_SYNCDATA)
# ... whether it is the last one (MDH_ACQEND)
# evalMDH() contains the correct and readable code for all mdh entries.
try:
# read everything and cut out the mdh
data_u8 = np.fromfile(fid, dtype=np.uint8, count=int(ulDMALength))
data_u8 = data_u8[mdhStart:]
except EOFError:
import warnings
warningString = f'\nAn unexpected read error occurred at this byte offset: {cPos} ({cPos / 1024 ** 3} GiB)\n'
warningString += 'Will stop reading now.\n'
warnings.warn(warningString)
isEOF = True
break
bitMask = data_u8[evIdx] # the initial 8 bit from evalInfoMask are enough
# print(bitMask)
if ((data_u8[0:3] == u8_000).all()) or (bitMask & bit_0):
# ok, look closer if really all *4* bytes are 0
data_u8[3] = bitget(data_u8[3], 0) # ubit24: keep only 1 bit from the 4th byte
tmp = data_u8[0:4]
tmp.dtype = np.uint32
ulDMALength = float(tmp)
if (ulDMALength == 0) or (bitMask & bit_0):
cPos = cPos + ulDMALength
# jump to next full 512 bytes
if cPos % 512:
cPos = cPos + 512 - cPos % 512
# isEOF = True
break
if (bitMask & bit_5): # MDH_SYNCDATA
data_u8[3] = bitget(data_u8[3], 0) # ubit24: keep only 1 bit from the 4th byte
tmp = data_u8[0:4]
tmp.dtype = np.uint32
ulDMALength = float(tmp)
cPos = cPos + ulDMALength
continue
# pehses: the pack bit indicates that multiple ADC are packed into one
# DMA, often in EPI scans (controlled by fRTSetReadoutPackaging in IDEA)
# since this code assumes one adc (x NCha) per DMA, we have to correct
# the "DMA length"
# if mdh.ulPackBit
# it seems that the packbit is not always set correctly
tmp = data_u8[dmaIdx]
tmp.dtype = np.uint16
NCol_NCha = tmp # was float [ushSamplesInScan ushUsedChannels]
ulDMALength = dmaOff + (8 * NCol_NCha[0] + dmaSkip) * NCol_NCha[1]
n_acq = n_acq + 1
# grow arrays in batches
if n_acq > szBlob:
grownArray = np.zeros((mdh_blob.shape[0], allocSize),
dtype=np.uint8) # pylint: disable=E1136 # pylint/issues/3139
mdh_blob = np.concatenate((mdh_blob, grownArray), axis=1)
filePos = np.concatenate((filePos, np.zeros((allocSize))), axis=0)
szBlob = mdh_blob.shape[1] # pylint: disable=E1136 # pylint/issues/3139
mdh_blob[:, n_acq - 1] = data_u8
filePos[n_acq - 1] = cPos
# progress = (cPos - measOffset) / measLength
t.update(np.float(str('%8.1f' % (cPos/1024**2))))
cPos = cPos + ulDMALength
t.close()
if isEOF:
n_acq = n_acq - 1 # ignore the last attempt
# import pdb; pdb.set_trace()
filePos[n_acq] = cPos
# discard overallocation:
mdh_blob = mdh_blob[:, :n_acq]
filePos = filePos[:n_acq] # in matlab was converted to row vector
# elapsed_time = time.time() - start
# print(f'{measLength / 1024 ** 2:8.1f}MB read in {elapsed_time:4.0f} s\n')
return mdh_blob, filePos, isEOF
def evalMDH(mdh_blob, version):
if version == 'vd':
isVD = True
mdh_blob = np.concatenate((mdh_blob[0:20, :], mdh_blob[40:, :]), axis=0) # remove 20 unnecessary bytes
else:
isVD = False
Nmeas = mdh_blob.shape[1]
ulPackBit = bitget(mdh_blob[3, :], 2)
ulPCI_rx = set_bit(mdh_blob[3, :], 7, False) # keep 6 relevant bits
ulPCI_rx = set_bit(ulPCI_rx, 8, False)
mdh_blob[3, :] = bitget(mdh_blob[3, :], 1) # ubit24: keep only 1 bit from the 4th byte
data_uint32 = np.ascontiguousarray(mdh_blob[0:76, :].transpose())
data_uint32.dtype = np.uint32
data_uint16 = np.ascontiguousarray(mdh_blob[28:, :].transpose())
data_uint16.dtype = np.uint16
data_single = np.ascontiguousarray(mdh_blob[68:, :].transpose())
data_single.dtype = np.single
@dataclass
class MDH: # byte pos
ulPackBit: np.uint8
ulPCI_rx: np.uint8
SlicePos: np.single
aushIceProgramPara: np.uint16
aushFreePara: np.uint16
lMeasUID: np.uint32 = data_uint32[:, 2 - 1] # 5 : 8
ulScanCounter: np.uint32 = data_uint32[:, 3 - 1] # 9 : 12
ulTimeStamp: np.uint32 = data_uint32[:, 4 - 1] # 13 : 16
ulPMUTimeStamp: np.uint32 = data_uint32[:, 5 - 1] # 17 : 20
aulEvalInfoMask: np.uint32 = data_uint32[:, 5:7] # 21 : 28
ushSamplesInScan: np.uint16 = data_uint16[:, 1 - 1] # 29 : 30
ushUsedChannels: np.uint16 = data_uint16[:, 2 - 1] # 31 : 32
sLC: np.uint16 = data_uint16[:, 2:16] # 33 : 60
sCutOff: np.uint16 = data_uint16[:, 16:18] # 61 : 64
ushKSpaceCentreColumn: np.uint16 = data_uint16[:, 19 - 1] # 66 : 66
ushCoilSelect: np.uint16 = data_uint16[:, 20 - 1] # 67 : 68
fReadOutOffcentre: np.single = data_single[:, 1 - 1] # 69 : 72
ulTimeSinceLastRF: np.uint32 = data_uint32[:, 19 - 1] # 73 : 76
ushKSpaceCentreLineNo: np.uint16 = data_uint16[:, 25 - 1] # 77 : 78
ushKSpaceCentrePartitionNo: np.uint16 = data_uint16[:, 26 - 1] # 79 : 80
if isVD:
mdh = MDH(ulPackBit, ulPCI_rx, data_single[:, 3:10], data_uint16[:, 40:64], data_uint16[:, 64:68])
else:
mdh = MDH(ulPackBit, ulPCI_rx, data_single[:, 7:14], data_uint16[:, 26:30], data_uint16[:, 30:34])
evalInfoMask1 = mdh.aulEvalInfoMask[:, 0]
@dataclass
class MASK:
MDH_ACQEND = np.minimum(evalInfoMask1 & 2 ** 0, 1)
MDH_RTFEEDBACK = np.minimum(evalInfoMask1 & 2 ** 1, 1)
MDH_HPFEEDBACK = np.minimum(evalInfoMask1 & 2 ** 2, 1)
MDH_SYNCDATA = np.minimum(evalInfoMask1 & 2 ** 5, 1)
MDH_RAWDATACORRECTION = np.minimum(evalInfoMask1 & 2 ** 10, 1)
MDH_REFPHASESTABSCAN = np.minimum(evalInfoMask1 & 2 ** 14, 1)
MDH_PHASESTABSCAN = np.minimum(evalInfoMask1 & 2 ** 15, 1)
MDH_SIGNREV = np.minimum(evalInfoMask1 & 2 ** 17, 1)
MDH_PHASCOR = np.minimum(evalInfoMask1 & 2 ** 21, 1)
MDH_PATREFSCAN = np.minimum(evalInfoMask1 & 2 ** 22, 1)
MDH_PATREFANDIMASCAN = np.minimum(evalInfoMask1 & 2 ** 23, 1)
MDH_REFLECT = np.minimum(evalInfoMask1 & 2 ** 24, 1)
MDH_NOISEADJSCAN = np.minimum(evalInfoMask1 & 2 ** 25, 1)
MDH_VOP = np.minimum(mdh.aulEvalInfoMask[:, 1] & 2 ** (53 - 32),
1) # WTC modified this as the original matlab code didn't make sense
MDH_IMASCAN = np.ones(Nmeas, dtype=np.uint32)
mask = MASK()
noImaScan = (mask.MDH_ACQEND | mask.MDH_RTFEEDBACK | mask.MDH_HPFEEDBACK
| mask.MDH_PHASCOR | mask.MDH_NOISEADJSCAN | mask.MDH_PHASESTABSCAN
| mask.MDH_REFPHASESTABSCAN | mask.MDH_SYNCDATA
| (mask.MDH_PATREFSCAN & ~mask.MDH_PATREFANDIMASCAN))
mask.MDH_IMASCAN -= noImaScan
return mdh, mask
# Overload 'dict' to enable dot access to keys
class AttrDict(dict):
def __init__(self, *args, **kwargs):
super(AttrDict, self).__init__(*args, **kwargs)
self.__dict__ = self
def mapVBVD(filename, **kwargs):
# parse kw arguments
bReadImaScan = kwargs.get('bReadImaScan', True)
bReadNoiseScan = kwargs.get('bReadNoiseScan', True)
bReadPCScan = kwargs.get('bReadPCScan', True)
bReadRefScan = kwargs.get('bReadRefScan', True)
bReadRefPCScan = kwargs.get('bReadRefPCScan', True)
bReadRTfeedback = kwargs.get('bReadRTfeedback', True)
bReadPhaseStab = kwargs.get('bReadPhaseStab', True)
bReadHeader = kwargs.get('bReadHeader', True)
ignoreROoffcenter = kwargs.get('ignoreROoffcenter', False)
# TODO: handle filename input variations
fid = open(filename, 'rb')
fid.seek(0, 2)
fileSize = fid.tell()
fid.seek(0, 0)
firstInt = np.fromfile(fid, dtype=np.uint32, count=1, offset=0)
secondInt = np.fromfile(fid, dtype=np.uint32, count=1, offset=0)
if (firstInt < 10000) & (secondInt <= 64):
version = 'vd'
print('Software version: VD')
# number of different scans in file stored in 2nd int
NScans = secondInt[0]
measID = np.fromfile(fid, dtype=np.uint32, count=1, offset=0)
fileID = np.fromfile(fid, dtype=np.uint32, count=1, offset=0)
measOffset = np.zeros(NScans, dtype=np.uint64)
measLength = np.zeros(NScans, dtype=np.uint64)
for k in range(NScans):
measOffset[k] = np.fromfile(fid, dtype=np.uint64, count=1, offset=0)
measLength[k] = np.fromfile(fid, dtype=np.uint64, count=1, offset=0)
fid.seek(152 - 16, 1)
else:
version = 'vb'
print('Software version: VB')
# in VB versions, the first 4 bytes indicate the beginning of the raw data part of the file
measOffset = np.zeros(1, dtype=np.uint64)
measLength = np.array([fileSize], dtype=np.uint64)
NScans = 1 # VB does not support multiple scans in one file
# Read data correction factors
# TODO: fill in for VB
if version == 'vb':
print('TODO')
# data will be read in two steps (two while loops):
# 1) reading all MDHs to find maximum line no., partition no.,... for
# ima, ref,... scan
# 2) reading the data
twix_obj = []
for s in range(NScans):
cPos = measOffset[s]
fid.seek(cPos, 0)
hdr_len = np.fromfile(fid, dtype=np.uint32, count=1, offset=0)
currTwixObj = AttrDict()
currTwixObjHdr = AttrDict()
# rstraj = 0
# read header
currTwixObjHdr, rstraj = read_twix_hdr(fid, currTwixObjHdr)
currTwixObj.update({'hdr': currTwixObjHdr})
# declare data objects:
mytmo = lambda dtype: twix_map_obj(dtype, filename, version, rstraj, *kwargs)
currTwixObj.update({'image': mytmo('image')})
currTwixObj.update({'noise': mytmo('noise')})
currTwixObj.update({'phasecor': mytmo('phasecor')})
currTwixObj.update({'phasestab': mytmo('phasestab')})
currTwixObj.update({'phasestab_ref0': mytmo('phasestab_ref0')})
currTwixObj.update({'phasestab_ref1': mytmo('phasestab_ref1')})
currTwixObj.update({'refscan': mytmo('refscan')})
currTwixObj.update({'refscan_phasecor': mytmo('refscan_phasecor')})
currTwixObj.update({'refscan_phasestab': mytmo('refscan_phasestab')})
currTwixObj.update({'refscan_phasestab_ref0': mytmo('refscan_phasestab_ref0')})
currTwixObj.update({'refscan_phasestab_ref1': mytmo('refscan_phasestab_ref1')})
currTwixObj.update({'rtfeedback': mytmo('rtfeedback')})
currTwixObj.update({'vop': mytmo('vop')})
# TODO: print reader version information
# if s == 0:
# # print(f'Reader version: {currTwixObj['image'].readerVersion})
# print('UTC: TODO')
# jump to first mdh
cPos += hdr_len
# print(cPos[0])
fid.seek(cPos[0], 0)
# print(f'Scan {s + 1}/{NScans}, read all mdhs:')
mdh_blob, filePos, isEOF = loop_mdh_read(fid, version, NScans, s, measOffset[s],
measLength[s]) # uint8; size: [ byteMDH Nmeas ]
cPos = filePos[-1]
# filePos = filePos[:-1]
# get mdhs and masks for each scan, no matter if noise, image, RTfeedback etc:
[mdh, mask] = evalMDH(mdh_blob, version)
# Assign mdhs to their respective scans and parse it in the correct twix objects.
# MDH_IMASCAN
isCurrScan = mask.MDH_IMASCAN.astype(bool)
if isCurrScan.any():
currTwixObj.image.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('image', None)
# MDH_NOISEADJSCAN
isCurrScan = mask.MDH_NOISEADJSCAN.astype(bool)
if isCurrScan.any():
currTwixObj.noise.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('noise', None)
# MDH_PATREFSCAN refscan
isCurrScan = (mask.MDH_PATREFSCAN | mask.MDH_PATREFANDIMASCAN) & ~(
mask.MDH_PHASCOR | mask.MDH_PHASESTABSCAN | mask.MDH_REFPHASESTABSCAN | mask.MDH_RTFEEDBACK | mask.MDH_HPFEEDBACK)
isCurrScan = isCurrScan.astype(bool)
if isCurrScan.any():
currTwixObj.refscan.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('refscan', None)
# MDH_RTFEEDBACK
isCurrScan = (mask.MDH_RTFEEDBACK | mask.MDH_HPFEEDBACK) & ~mask.MDH_VOP
isCurrScan = isCurrScan.astype(bool)
if isCurrScan.any():
currTwixObj.rtfeedback.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('rtfeedback', None)
# VOP
isCurrScan = (mask.MDH_RTFEEDBACK & mask.MDH_VOP)
isCurrScan = isCurrScan.astype(bool)
if isCurrScan.any():
currTwixObj.vop.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('vop', None)
# MDH_PHASCOR
isCurrScan = mask.MDH_PHASCOR & (~mask.MDH_PATREFSCAN | mask.MDH_PATREFANDIMASCAN)
isCurrScan = isCurrScan.astype(bool)
if isCurrScan.any():
currTwixObj.phasecor.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('phasecor', None)
# refscanPC
isCurrScan = mask.MDH_PHASCOR & (mask.MDH_PATREFSCAN | mask.MDH_PATREFANDIMASCAN)
isCurrScan = isCurrScan.astype(bool)
if isCurrScan.any():
currTwixObj.refscan_phasecor.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('refscan_phasecor', None)
# phasestab MDH_PHASESTABSCAN
isCurrScan = (mask.MDH_PHASESTABSCAN & ~mask.MDH_REFPHASESTABSCAN) & (
~mask.MDH_PATREFSCAN | mask.MDH_PATREFANDIMASCAN)
isCurrScan = isCurrScan.astype(bool)
if isCurrScan.any():
currTwixObj.phasestab.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('phasestab', None)
# refscanPS MDH_PHASESTABSCAN
isCurrScan = (mask.MDH_PHASESTABSCAN & ~mask.MDH_REFPHASESTABSCAN) & (
mask.MDH_PATREFSCAN | mask.MDH_PATREFANDIMASCAN)
isCurrScan = isCurrScan.astype(bool)
if isCurrScan.any():
currTwixObj.refscan_phasestab.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('refscan_phasestab', None)
# phasestabRef0 MDH_PHASESTABSCAN
isCurrScan = (mask.MDH_REFPHASESTABSCAN & ~mask.MDH_PHASESTABSCAN) & (
~mask.MDH_PATREFSCAN | mask.MDH_PATREFANDIMASCAN)
isCurrScan = isCurrScan.astype(bool)
if isCurrScan.any():
currTwixObj.phasestab_ref0.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('phasestab_ref0', None)
# refscanPSRef0 MDH_PHASESTABSCAN
isCurrScan = (mask.MDH_REFPHASESTABSCAN & ~mask.MDH_PHASESTABSCAN) & (
mask.MDH_PATREFSCAN | mask.MDH_PATREFANDIMASCAN)
isCurrScan = isCurrScan.astype(bool)
if isCurrScan.any():
currTwixObj.refscan_phasestab_ref0.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('refscan_phasestab_ref0', None)
# phasestabRef1 MDH_PHASESTABSCAN
isCurrScan = (mask.MDH_REFPHASESTABSCAN & mask.MDH_PHASESTABSCAN) & (
~mask.MDH_PATREFSCAN | mask.MDH_PATREFANDIMASCAN)
isCurrScan = isCurrScan.astype(bool)
if isCurrScan.any():
currTwixObj.phasestab_ref1.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('phasestab_ref1', None)
# refscanPSRef1 MDH_PHASESTABSCAN
isCurrScan = (mask.MDH_REFPHASESTABSCAN & mask.MDH_PHASESTABSCAN) & (
mask.MDH_PATREFSCAN | mask.MDH_PATREFANDIMASCAN)
isCurrScan = isCurrScan.astype(bool)
if isCurrScan.any():
currTwixObj.refscan_phasestab_ref1.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('refscan_phasestab_ref1', None)
# if isEOF:
# # recover from read error
# # for keys in currTwixObj:
# # currTwixObj[keys].tryAndFixLastMdh()
# print('tryAndFixLastMdh not yet implemented')
# # pass
# else:
# for k in currTwixObj:
# if k != 'hdr':
# currTwixObj.k.clean()
twix_obj.append(currTwixObj)
fid.close()
if len(twix_obj) == 1:
twix_obj = twix_obj[0]
return twix_obj
mapVBVD/read_twix_hdr.py deleted 100644 → 0
View file @ 6029b436
import re
import numpy as np
from scipy.integrate import cumtrapz
from itertools import chain
class AttrDict(dict):
def __init__(self, *args, **kwargs):
super(AttrDict, self).__init__(*args, **kwargs)
self.__dict__ = self
def parse_ascconv(buffer):
# print(buffer)
vararray = re.finditer(r'(?P<name>\S*)\s*=\s*(?P<value>\S*)\n', buffer)
# print(vararray)
mrprot = AttrDict()
for v in vararray:
try:
value = float(v.group('value'))
except ValueError:
value = v.group('value')
# now split array name and index (if present)
vvarray = re.finditer(r'(?P<name>\w+)(\[(?P<ix>[0-9]+)\])?', v.group('name'))
currKey = []
for vv in vvarray:
# print(vv.group('name'))
currKey.append(vv.group('name'))
if vv.group('ix') is not None:
# print(vv.group('ix'))
currKey.append(vv.group('ix'))
mrprot.update({tuple(currKey): value})
return mrprot