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Commit 576f3ccf authored by Mo Shahdloo's avatar Mo Shahdloo
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post-merge fixes

parent 4af385d4
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mapVBVD/__init__.py
View file @ 576f3ccf
from mapVBVD.mapVBVD import mapVBVD
from mapVBVD.read_twix_hdr import read_twix_hdr
from mapVBVD.twix_map_obj import twix_map_obj
from ._version import get_versions
__version__ = get_versions()['version']
del get_versions
mapVBVD/_version.py
View file @ 576f3ccf
......@@ -43,7 +43,7 @@ def get_config():
cfg.style = "pep440"
cfg.tag_prefix = ""
cfg.parentdir_prefix = ""
cfg.versionfile_source = "mapVBVD/_version.py"
cfg.versionfile_source = "core/_version.py"
cfg.verbose = False
return cfg
......
mapVBVD/mapVBVD.py
View file @ 576f3ccf
import numpy as np
from dataclasses import dataclass,field
import mapVBVD as pkg
from mapVBVD.read_twix_hdr import read_twix_hdr
from mapVBVD.twix_map_obj import twix_map_obj
from dataclasses import dataclass, field
from core import mapVBVD as pkg
from attrdict import AttrDict, AttrMap, AttrDefault
from tqdm import tqdm, trange
......@@ -65,7 +63,8 @@ def loop_mdh_read(fid, version, Nscans, scan, measOffset, measLength):
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)
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)
......@@ -129,18 +128,18 @@ def loop_mdh_read(fid, version, Nscans, scan, measOffset, measLength):
# 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)
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
filePos = np.concatenate((filePos, np.zeros((allocSize))), axis=0)
t.update(np.float(str('%8.1f' % (cPos/1024**2))))
szBlob = mdh_blob.shape[1] # pylint: disable=E1136 # pylint/issues/3139
mdh_blob[:, n_acq - 1] = data_u8
filePos[n_acq - 1] = cPos
t.update(np.float(str('%8.1f' % (cPos / 1024 ** 2))))
cPos = cPos + ulDMALength
......@@ -238,8 +237,8 @@ def evalMDH(mdh_blob, version):
mask.MDH_IMASCAN -= noImaScan
def mapVBVD(filename, quiet=False, **kwargs):
def mapVBVD(filename, quiet=False, **kwargs):
if not quiet:
print(f'pymapVBVD version {pkg.__version__}')
......@@ -281,7 +280,7 @@ def mapVBVD(filename, quiet=False, **kwargs):
fid.seek(152 - 16, 1)
else:
version = 'vb'
version = 'vb'
if not quiet:
print('Software version: VB')
......@@ -342,7 +341,7 @@ def mapVBVD(filename, quiet=False, **kwargs):
# print(f'Scan {s + 1}/{NScans}, read all mdhs:')
mdh_blob, filePos, isEOF = loop_mdh_read(fid, version, NScans, s, measOffset[s],
measLength[s],print_prog= not quiet) # uint8; size: [ byteMDH Nmeas ]
measLength[s], print_prog=not quiet) # uint8; size: [ byteMDH Nmeas ]
cPos = filePos[-1]
# filePos = filePos[:-1]
......@@ -459,10 +458,10 @@ def mapVBVD(filename, quiet=False, **kwargs):
if isCurrScan.any():
currTwixObj.refscan_phasestab_ref1.readMDH(mdh, filePos, isCurrScan)
else:
currTwixObj.pop('refscan_phasestab_ref1',None)
currTwixObj.pop('refscan_phasestab_ref1', None)
if isEOF:
#recover from read error
# recover from read error
for keys in currTwixObj:
if keys != 'hdr':
currTwixObj[keys].tryAndFixLastMdh()
......@@ -470,24 +469,24 @@ def mapVBVD(filename, quiet=False, **kwargs):
for keys in currTwixObj:
if keys != 'hdr':
currTwixObj[keys].clean()
twix_obj.append(myAttrDict(currTwixObj))
fid.close()
if len(twix_obj) == 1:
twix_obj = twix_obj[0]
# breakpoint()
return twix_obj
return twix_obj
# Add some class methods to AttrDict so that we get around the issue of not being able to
# access methods of objects accessed as attributes.
class myAttrDict(AttrDict):
def __init__(self,*args):
def __init__(self, *args):
super().__init__(*args)
def search_header_for_keys(self,*args,**kwargs):
def search_header_for_keys(self, *args, **kwargs):
"""Search header keys for terms.
Accesses search_for_keys method in header.
......@@ -496,18 +495,18 @@ class myAttrDict(AttrDict):
regex (optional) : Search using regex or for exact strings.
top_lvl (optional) : Specify list of parameter sets to search (e.g. YAPS)
print_flag(optional): If False no output will be printed.
"""
return self['hdr'].search_for_keys(*args,**kwargs)
"""
return self['hdr'].search_for_keys(*args, **kwargs)
def search_header_for_val(self,top_lvl,keys,**kwargs):
def search_header_for_val(self, top_lvl, keys, **kwargs):
"""Return values for keys found using search terms for terms.
Args:
top_lvl : Specify list of parameter sets to search (e.g. YAPS)
keys : search terms as list of strings.
regex (optional): Search using regex or for exact strings.
"""
keys = self['hdr'].search_for_keys(keys,print_flag=False,top_lvl=top_lvl,**kwargs)
"""
keys = self['hdr'].search_for_keys(keys, print_flag=False, top_lvl=top_lvl, **kwargs)
out_vals = []
for key in keys:
......@@ -521,4 +520,3 @@ class myAttrDict(AttrDict):
MDH = list(self.keys())
MDH.pop(MDH.index('hdr'))
return MDH
mapVBVD/twix_map_obj.py
View file @ 576f3ccf
......@@ -6,6 +6,7 @@ import time
from tqdm import tqdm, trange
import logging
class twix_map_obj:
@property
......@@ -228,29 +229,30 @@ class twix_map_obj:
self.skipToFirstLine = False
else:
self.skipToFirstLine = True
def __str__(self):
des_str = ('***twix_map_obj***\n'
f'File: {self.filename}\n'
f'Software: {self.softwareVersion}\n'
f'Number of acquisitions read {self.NAcq}\n'
f'Data size is {np.array2string(self.fullSize,formatter={"float":lambda x: "%.0f" % x},separator=",")}\n'
f'Squeezed data size is {np.array2string(self.sqzSize(),formatter={"int":lambda x: "%i" % x},separator=",")} ({self.sqzDims()})\n'
f'NCol = {self.NCol:0.0f}\n'
f'NCha = {self.NCha:0.0f}\n'
f'NLin = {self.NLin:0.0f}\n'
f'NAve = {self.NAve:0.0f}\n'
f'NSli = {self.NSli:0.0f}\n'
f'NPar = {self.NPar:0.0f}\n'
f'NEco = {self.NEco:0.0f}\n'
f'NPhs = {self.NPhs:0.0f}\n'
f'NRep = {self.NRep:0.0f}\n'
f'NSet = {self.NSet:0.0f}\n'
f'NSeg = {self.NSeg:0.0f}\n'
f'NIda = {self.NIda:0.0f}\n'
f'NIdb = {self.NIdb:0.0f}\n'
f'NIdc = {self.NIdc:0.0f}\n'
f'NIdd = {self.NIdd:0.0f}\n'
f'NIde = {self.NIde:0.0f}')
f'File: {self.filename}\n'
f'Software: {self.softwareVersion}\n'
f'Number of acquisitions read {self.NAcq}\n'
f'Data size is {np.array2string(self.fullSize, formatter={"float": lambda x: "%.0f" % x}, separator=",")}\n'
f'Squeezed data size is {np.array2string(self.sqzSize(), formatter={"int": lambda x: "%i" % x}, separator=",")} ({self.sqzDims()})\n'
f'NCol = {self.NCol:0.0f}\n'
f'NCha = {self.NCha:0.0f}\n'
f'NLin = {self.NLin:0.0f}\n'
f'NAve = {self.NAve:0.0f}\n'
f'NSli = {self.NSli:0.0f}\n'
f'NPar = {self.NPar:0.0f}\n'
f'NEco = {self.NEco:0.0f}\n'
f'NPhs = {self.NPhs:0.0f}\n'
f'NRep = {self.NRep:0.0f}\n'
f'NSet = {self.NSet:0.0f}\n'
f'NSeg = {self.NSeg:0.0f}\n'
f'NIda = {self.NIda:0.0f}\n'
f'NIdb = {self.NIdb:0.0f}\n'
f'NIdc = {self.NIdc:0.0f}\n'
f'NIdd = {self.NIdd:0.0f}\n'
f'NIde = {self.NIde:0.0f}')
return des_str
def __repr__(self):
......@@ -313,10 +315,10 @@ class twix_map_obj:
isLastAcqGood = False
cnt = 0
while not isLastAcqGood and self.NAcq > 0 and cnt < 100:
while not isLastAcqGood and self.NAcq > 0 and cnt < 100:
try:
self.clean()
self.unsorted(self.NAcq)
self.unsorted(self.NAcq)
isLastAcqGood = True
except Exception as e:
logging.exception(f'An error occurred whilst trying to fix last MDH. NAcq = {self.NAcq:.0f}')
......@@ -326,45 +328,45 @@ class twix_map_obj:
cnt += 1
def clean(self):
#Cut mdh data to actual size. Maybe we rejected acquisitions at the end
#due to read errors.
if self.NAcq==0:
# Cut mdh data to actual size. Maybe we rejected acquisitions at the end
# due to read errors.
if self.NAcq == 0:
return
fields = ['NCol', 'NCha',
'Lin', 'Par', 'Sli', 'Ave', 'Phs', 'Eco', 'Rep',
'Set', 'Seg', 'Ida', 'Idb', 'Idc', 'Idd', 'Ide',
'centerCol' , 'centerLin', 'centerPar', 'cutOff',
'coilSelect' , 'ROoffcenter', 'timeSinceRF', 'IsReflected',
'scancounter', 'timestamp', 'pmutime', 'IsRawDataCorrect',
'slicePos' , 'iceParam', 'freeParam', 'memPos']
'centerCol', 'centerLin', 'centerPar', 'cutOff',
'coilSelect', 'ROoffcenter', 'timeSinceRF', 'IsReflected',
'scancounter', 'timestamp', 'pmutime', 'IsRawDataCorrect',
'slicePos', 'iceParam', 'freeParam', 'memPos']
nack = self.NAcq
idx = np.arange(0,nack-1)
idx = np.arange(0, nack - 1)
for f in fields:
curr = getattr(self,f)
if curr.shape[0] > nack: # rarely
curr = getattr(self, f)
if curr.shape[0] > nack: # rarely
print('Here')
setattr(self, f, curr[idx]) # 1st dim: samples, 2nd dim acquisitions
self.NLin = np.max(self.Lin)+1 #+1 so that size isn't 0
self.NPar = np.max(self.Par)+1
self.NSli = np.max(self.Sli)+1
self.NAve = np.max(self.Ave)+1
self.NPhs = np.max(self.Phs)+1
self.NEco = np.max(self.Eco)+1
self.NRep = np.max(self.Rep)+1
self.NSet = np.max(self.Set)+1
self.NSeg = np.max(self.Seg)+1
self.NIda = np.max(self.Ida)+1
self.NIdb = np.max(self.Idb)+1
self.NIdc = np.max(self.Idc)+1
self.NIdd = np.max(self.Idd)+1
self.NIde = np.max(self.Ide)+1
#ok, let us assume for now that all NCol and NCha entries are
#the same for all mdhs:
setattr(self, f, curr[idx]) # 1st dim: samples, 2nd dim acquisitions
self.NLin = np.max(self.Lin) + 1 # +1 so that size isn't 0
self.NPar = np.max(self.Par) + 1
self.NSli = np.max(self.Sli) + 1
self.NAve = np.max(self.Ave) + 1
self.NPhs = np.max(self.Phs) + 1
self.NEco = np.max(self.Eco) + 1
self.NRep = np.max(self.Rep) + 1
self.NSet = np.max(self.Set) + 1
self.NSeg = np.max(self.Seg) + 1
self.NIda = np.max(self.Ida) + 1
self.NIdb = np.max(self.Idb) + 1
self.NIdc = np.max(self.Idc) + 1
self.NIdd = np.max(self.Idd) + 1
self.NIde = np.max(self.Ide) + 1
# ok, let us assume for now that all NCol and NCha entries are
# the same for all mdhs:
# WTC not sure if this is a good idea - will keep the same as original for now
if self.NCol.ndim > 0:
......@@ -459,7 +461,7 @@ class twix_map_obj:
outSize[k] = selRange[cDim].size
for r,s in zip(selRange,self.dataSize()):
for r, s in zip(selRange, self.dataSize()):
if np.max(r) > s:
raise Exception('selection out of range')
# To implement indexing
......@@ -504,7 +506,7 @@ class twix_map_obj:
def unsorted(self, ival=None):
# returns the unsorted data [NCol,NCha,#samples in acq. order]
if ival:
mem = np.atleast_1d(self.memPos[ival-1])
mem = np.atleast_1d(self.memPos[ival - 1])
else:
mem = self.memPos
out = self.readData(mem)
......@@ -622,27 +624,27 @@ class twix_map_obj:
fid = open(self.filename, 'rb')
return fid
def readData(self,mem,cIxToTarg=None,cIxToRaw=None,selRange=None,selRangeSz=None,outSize=None):
def readData(self, mem, cIxToTarg=None, cIxToRaw=None, selRange=None, selRangeSz=None, outSize=None):
mem = mem.astype(int)
if outSize is None:
if selRange is None:
selRange = [np.arange(0,self.dataSize()[0]).astype(int),np.arange(0,self.dataSize()[1]).astype(int)]#[slice(None,None,None),slice(None,None,None)]
selRange = [np.arange(0, self.dataSize()[0]).astype(int), np.arange(0, self.dataSize()[1]).astype(
int)] # [slice(None,None,None),slice(None,None,None)]
else:
selRange[0] = np.arange(0,self.dataSize()[0]).astype(int) #slice(None,None,None)
selRange[1] = np.arange(0,self.dataSize()[0]).astype(int) #slice(None,None,None)
outSize = np.append(self.dataSize()[0:2],mem.size).astype(int)
selRange[0] = np.arange(0, self.dataSize()[0]).astype(int) # slice(None,None,None)
selRange[1] = np.arange(0, self.dataSize()[0]).astype(int) # slice(None,None,None)
outSize = np.append(self.dataSize()[0:2], mem.size).astype(int)
selRangeSz = outSize
cIxToTarg = np.arange(0,selRangeSz[2])
cIxToRaw = cIxToTarg
cIxToTarg = np.arange(0, selRangeSz[2])
cIxToRaw = cIxToTarg
# else:
# if np.array_equiv(selRange[0],np.arange(0,self.dataSize()[0]).astype(int)):
# selRange[0] = slice(None,None,None)
# if np.array_equiv(selRange[1],np.arange(0,self.dataSize()[1]).astype(int)):
# selRange[1] = slice(None,None,None)
out = np.zeros(outSize, dtype=np.csingle)
out = out.reshape((selRangeSz[0], selRangeSz[1], -1))
......@@ -653,7 +655,7 @@ class twix_map_obj:
readSize = self.freadInfo.sz.astype(int)
readShape = self.freadInfo.shape.astype(int)
readCut = self.freadInfo.cut.astype(int)
keepOS = np.concatenate([list(range(int(self.NCol/4))), list(range(int(self.NCol*3/4), int(self.NCol)))])
keepOS = np.concatenate([list(range(int(self.NCol / 4))), list(range(int(self.NCol * 3 / 4), int(self.NCol)))])
bIsReflected = self.IsReflected[cIxToRaw]
bRegrid = self.regrid and self.rampSampTrj.size > 1
......@@ -772,7 +774,8 @@ class twix_map_obj:
x, y = np.meshgrid(src_grid[1], src_grid[0])
# NOTE: there is some minor differences in regridding precision between python and matlab, don't
# expect the same result from regridding
block = np.reshape(griddata((x.ravel(), y.ravel()), z.ravel(), (xi, yi), method='cubic'), sz, order='F')
block = np.reshape(griddata((x.ravel(), y.ravel()), z.ravel(), (xi, yi), method='cubic'), sz,
order='F')
if self.removeOS:
block = np.fft.fft(
......
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