def loadProjDefinitionFile(argServer, inputFileName=None, exptName=None):
# parse input file
if inputFileName is None:
inputFileName = argServer.getFile()
if inputFileName:
fileData = genUtil.parseBrukerSummary(inputFileName)
else:
return
# get format specifier
format = fileData.get('FORMAT')
if format not in supportedFormats:
print("ERROR Unknown format; %s. Supported formats: %s" %
(format, supportedFormats))
# get OpenSpectrum popup and set up
top = argServer.parent
open_spectra = top.popups.get('open_spectrum')
if open_spectra is None:
top.openPopup('open_spectrum', OpenSpectrum.OpenSpectrumPopup)
open_spectra = top.popups.get('open_spectrum')
open_spectra.verifySelect.setSelected(False)
open_spectra.sharedExpSelect.setSelected(True)
# set up data structures
extraData = {}
specNames = []
fileNames = []
scalingFactors = []
useScalingFactors = False
if format == 'Bruker':
keepDirectories = 4
dimParNameMap = {
'NUCLEI': 'displayNames',
#'SW_ppm':'swppm',
#'SW_hz':'sw',
#'O1_ppm':'carppm',
}
# set up special data
numDims = None
for tagin, tagout in dimParNameMap.items():
val = fileData.get(tagin)
if val is not None:
if numDims is None:
numDims = len(val)
elif numDims != len(val):
print("ERROR for %s: numDims inconsistent, should be %d" %
(tagin, numDims))
return
extraData[tagout] = val
# get file and base directory
ll = []
for tt in fileData.items():
try:
ind = int(tt[0])
# this is a string form of an integer. Use it
ll.append((ind, tt))
except ValueError:
# not a string form of an integer - skip
continue
for xx in sorted(ll):
tt = xx[1]
specName, dd = tt
fileName = dd.get('PATH')
if fileName:
specNames.append(str(specName))
fileNames.append(fileName)
scalingFactor = dd.get('DEFINITION')
if scalingFactor:
if numDims is None:
# always the case first time for now, but the code might change
numDims = len(scalingFactor)
if len(scalingFactor) == numDims:
useScalingFactors = True
else:
scalingFactor = None
else:
scalingFactor = None
scalingFactors.append(scalingFactor)
#indx = list(OpenSpectrum.file_formats).index('Bruker')
#open_spectra.formatPulldown.setSelectedIndex(indx)
#open_spectra.chooseFormat(indx,'Bruker')
open_spectra.formatPulldown.set('Bruker')
open_spectra.chooseFormat('Bruker')
else:
return
# find and set set selection directory
#baseDir = uniIo.commonSuperDirectory(*fileNames)
startDir = os.path.dirname(inputFileName)
baseDir, paths = uniIo.suggestFileLocations(fileNames, startDir=startDir)
if baseDir is None:
print 'WARNING, described files not found. Aborting'
fileNames = [os.path.join(baseDir, path) for path in paths]
defaultExpName = os.path.basename(baseDir)
open_spectra.fileSelect.changeDir(baseDir)
# set 'Spectra to open' matrix:
objectList = []
textMatrix = []
# get experiment name
if exptName is None:
exptName = argServer.askString(message='New Experiment Name',
default=defaultExpName)
#exptName = defaultExpName
shiftListName = open_spectra.getShiftLists()[0]
windowOpt = 1
for ii, specName in enumerate(specNames):
path = paths[ii]
optString = OpenSpectrum.WINDOW_OPTS[windowOpt]
textMatrix.append([exptName, specName, path, optString, shiftListName])
objectList.append([exptName, specName, path, windowOpt, shiftListName])
if len(fileNames) > 1:
open_spectra.openButton.config(text='Open Spectra')
else:
open_spectra.openButton.config(text='Open Spectrum')
open_spectra.scrolledMatrix.update(objectList=objectList,
textMatrix=textMatrix)
if useScalingFactors:
extraData['scalingFactors'] = scalingFactors[0]
refSpec = open_spectra.openSpectrum(exptName,
specNames[0],
fileNames[0],
extraData=extraData)
if not refSpec:
return
refExp = refSpec.experiment
# set up internal Analysis data
open_spectra.parent.finishInitSpectrum(refSpec)
print 'finished opening spectrum', refExp.name, refSpec.name
refDataStore = refSpec.dataStore
preferDataUrls = [refDataStore.dataUrl]
memopsRoot = refSpec.root
expDimRefs = [
xdr for xd in refExp.sortedExpDims() for xdr in xd.sortedExpDimRefs()
]
#
for ii, fullPath in enumerate(fileNames):
if ii == 0:
# skip first
continue
if useScalingFactors:
scalingFactor = scalingFactors[ii]
else:
scalingFactor = None
# get new DataLocationStore
useDataUrl, filePath = getDataStoringFromFilepath(
memopsRoot,
fullPath,
preferDataUrls=preferDataUrls,
keepDirectories=keepDirectories)
# get data file name from entry path
if format == 'Bruker':
from ccp.format.bruker.generalIO import getMatrixFilePath
urlPath = os.path.join(useDataUrl.url.dataLocation, '')
dataPath = getMatrixFilePath(os.path.join(urlPath, filePath),
refDataStore.numDims)
path = dataPath[len(urlPath):]
elif format == 'Azara':
raise NotImplementedError(
"Azara type projection series not yet implemented")
else:
path = filePath
copyPars = {'dataUrl': useDataUrl, 'path': path, 'nmrDataSources': []}
newDataStore = copySubTree(refDataStore,
refDataStore.dataLocationStore,
topObjectParameters=copyPars)
# get new spectrum
copyPars = {'name': specNames[ii], 'dataStore': newDataStore}
newSpectrum = copySubTree(refSpec,
refExp,
topObjectParameters=copyPars)
if useScalingFactors:
dataDims = newSpectrum.sortedDataDims()
lastDataDim = dataDims[-1]
startAt = len(dataDims) - 1
for jj in range(len(dataDims) - 1, len(scalingFactor)):
expDimRef = expDimRefs[jj]
dimScaling = lastDataDim.findFirstDimensionScaling(
expDimRef=expDimRef)
if dimScaling is None:
lastDataDim.newDimensionScaling(
scalingFactors=(scalingFactor[jj], ),
expDimRef=expDimRef)
else:
dimScaling.scalingFactors = (scalingFactor[jj], )
# set up internal Analysis data
open_spectra.parent.visibleSpectra[newSpectrum] = False
open_spectra.parent.finishInitSpectrum(newSpectrum)
print 'finished opening spectrum', refExp.name, newSpectrum.name
print
print 'Projection spectra loaded into experiment', refExp.name
def loadProject(parent, path, projectName=None):
path = uniIo.normalisePath(path)
askdir = lambda title, prompt, initial_value: askDir(
title, prompt, initial_value, parent=parent, extra_dismiss_text='Skip')
askfile = lambda title, prompt, initial_value: askFile(
title, prompt, initial_value, parent=parent, extra_dismiss_text='Skip')
project = genIo.loadProject(path,
showWarning=showWarning,
askDir=askdir,
askFile=askfile)
# now check dataStores
# delete those that are not used
# and otherwise check path to see if exists
dataStores = []
for dataLocationStore in project.dataLocationStores:
for dataStore in dataLocationStore.dataStores:
if isinstance(dataStore,
NumericMatrix) and not dataStore.nmrDataSources:
print 'deleting dataStore %s with path %s' % (
dataStore, dataStore.fullPath)
dataStore.delete()
elif isinstance(
dataStore,
MimeTypeDataStore) and not dataStore.nmrDataSourceImages:
print 'deleting dataStore %s with path %s' % (
dataStore, dataStore.fullPath)
dataStore.delete()
else:
dataStores.append(dataStore)
badDataStores = [
dataStore for dataStore in dataStores
if not os.path.exists(dataStore.fullPath)
]
if badDataStores:
# find DataUrls involved
dataUrls = set(dataStore.dataUrl for dataStore in badDataStores)
startDir = project.packageLocator.findFirstRepository(
).url.dataLocation
for dataUrl in dataUrls:
if not dataUrl.dataStores.difference(badDataStores):
# all DataStores for this DataUrl are bad
# we can make changes without affecting 'good' DataStores
# Look for an obvious place the data may have moved to
dataStores = dataUrl.sortedDataStores()
fullPaths = [dataStore.fullPath for dataStore in dataStores]
baseDir, newPaths = uniIo.suggestFileLocations(
fullPaths, startDir=startDir)
if baseDir is not None:
# We have a file location that fits all missing files.
# Change dataStores to use it
print 'WARNING, resetting data locations to: \n%s\n' % baseDir
ccpGenIo.changeDataStoreUrl(dataStores[0], baseDir)
for ii, dataStore in enumerate(dataStores):
dataStore.path = newPaths[ii]
if [
dataStore for dataStore in dataStores
if not os.path.exists(dataStore.fullPath)
]:
popup = DataLocationPopup(parent, project, modal=True)
popup.destroy()
return project
