示例#1
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def load_contrasts_from_mat(spm_mat_file):
    """Returns a dictionary from an SPM.mat file of contrasts and the string
    linear combination of conditions for the corresponding contrast.

    Parameter
    ---------
    spm_mat_file : string
        path to the SPM.mat file to load contrasts from

    Returns
    -------
    contrasts : dict
        dictionary of {contrast_name: linear_condition_combination}
    """

    spm = loadmat(spm_mat_file)
    spm = spm["SPM"]

    conditions = get_conditions_list_from_mat(spm)
    contrasts_vect = get_contrasts(spm)

    return OrderedDict(
        (clean_string_for_xml(str(contrast[0][0])),
         contrast_vec_to_name(contrast[1][:len(conditions)], conditions))
        for contrast in contrasts_vect if str(contrast[2][0]) == "T")
示例#2
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def load_data(thefile):
    print "Loading data ..."
    matfile  = mio.loadmat(thefile)
    data     = matfile["data"]
    triggers = matfile["triggers"]
    
    return data, triggers
示例#3
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文件: spmio.py 项目: pyhrf/pyhrf
def load_contrasts_from_mat(spm_mat_file):
    """Returns a dictionary from an SPM.mat file of contrasts and the string
    linear combination of conditions for the corresponding contrast.

    Parameter
    ---------
    spm_mat_file : string
        path to the SPM.mat file to load contrasts from

    Returns
    -------
    contrasts : dict
        dictionary of {contrast_name: linear_condition_combination}
    """

    spm = loadmat(spm_mat_file)
    spm = spm["SPM"]

    conditions = get_conditions_list_from_mat(spm)
    contrasts_vect = get_contrasts(spm)

    return OrderedDict(
        (clean_string_for_xml(str(contrast[0][0])), contrast_vec_to_name(contrast[1][: len(conditions)], conditions))
        for contrast in contrasts_vect
        if str(contrast[2][0]) == "T"
    )
示例#4
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 def _check_case(self, name, files, case):
     for file_name in files:
         matdict = loadmat(file_name)
         label = "test %s; file %s" % (name, file_name)
         for k, expected in case.items():
             k_label = "%s, variable %s" % (label, k)
             assert k in matdict, "Missing key at %s" % k_label
             self._check_level(k_label, expected, matdict[k])
示例#5
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def flickr_spectral_clustering(matfilename):
    
    myhash = loadmat(matfilename)

    data = myhash['data']
    data = exp(data +(random([len(data), len(data)]))*0.0001) # - 0.00005)
    keys = myhash['names']

    #maxval = max(data)
    #data = max_val-data+(randn(len(data), len(data))*0.0001)


    classes, k = spectral_clustering_W(data, 20) 

    for i in range(k):
        print "*************"
        for j in range(len(classes)):
            if(i == int(classes[j])):
                print keys[j]
示例#6
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def load_regnames(spmMatFile):
    d = loadmat(spmMatFile)
    spm = d['SPM']
    return [s[0] for s in spm['xX'][0, 0]['name'][0, 0][0]]
示例#7
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def load_scalefactor_from_mat(spmMatFile):
    d = loadmat(spmMatFile)
    spm = d['SPM']
    return float(get_field(get_field(spm, 'xGX')[0][0], 'gSF')[0][0][0][0])
示例#8
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	def readHeader(self):
		self.h=loadmat(self.headerFilename)
示例#9
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文件: spmio.py 项目: Solvi/pyhrf
def load_scalefactor_from_mat(spmMatFile):
    d = loadmat(spmMatFile)
    spm = d['SPM']
    return float(get_field(get_field(spm,'xGX')[0][0],'gSF')[0][0][0][0])
示例#10
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文件: spmio.py 项目: Solvi/pyhrf
def load_contrasts(spmMatFile):
    d = loadmat(spmMatFile)
    spm = d['SPM']
    return get_constrasts(spm)
示例#11
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文件: spmio.py 项目: Solvi/pyhrf
def load_paradigm_from_mat(spmMatFile):
    d = loadmat(spmMatFile)
    spm = d['SPM']    
    return (get_onsets_from_spm_dict(spm), get_tr_from_spm_dict(spm))
示例#12
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    #pp1 = wpwr(data_mean)[0]
    #p2 = wpwr(data_tspca)[0]
    #pp2 = wpwr(data_tspca_mean)[0]

    #print "TSPCA done. ", 100*p2/p1, " of raw power remains"
    #print "trial-averaged: ", 100*pp2/pp1, " of raw power remains"

    # apply SNS
    nneighbors = 10
    print 'SNS ...'
    data_tspca_sns = sns(data_tspca, nneighbors)

    # apply DSS

    print "DSS ..."
    ## Keep all PC components
    data_tspca_sns = demean(data_tspca_sns)[0]
    todss, fromdss, ratio, pwr = dss1(data_tspca_sns)
    ## c3 = DSS components
    data_tspca_sns_dss = fold(dot(unfold(data_tspca_sns), todss),
                              data_tspca_sns.shape[0])

    return data_tspca_sns


x = mio.loadmat('data2.mat')
data = x['data']
ref = x['ref']

cleandata = clean(data, ref)
示例#13
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    # p1 = wpwr(data)[0]
    # pp1 = wpwr(data_mean)[0]
    # p2 = wpwr(data_tspca)[0]
    # pp2 = wpwr(data_tspca_mean)[0]

    # print "TSPCA done. ", 100*p2/p1, " of raw power remains"
    # print "trial-averaged: ", 100*pp2/pp1, " of raw power remains"

    # apply SNS
    nneighbors = 10
    print "SNS ..."
    data_tspca_sns = sns(data_tspca, nneighbors)

    # apply DSS

    print "DSS ..."
    ## Keep all PC components
    data_tspca_sns = demean(data_tspca_sns)[0]
    todss, fromdss, ratio, pwr = dss1(data_tspca_sns)
    ## c3 = DSS components
    data_tspca_sns_dss = fold(dot(unfold(data_tspca_sns), todss), data_tspca_sns.shape[0])

    return data_tspca_sns


x = mio.loadmat("data2.mat")
data = x["data"]
ref = x["ref"]

cleandata = clean(data, ref)
示例#14
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	def readData(self):
		self.d=loadmat(self.dataFilename)
		self.tvec=arange(len(self.d['di0']))*0.04
示例#15
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文件: spmio.py 项目: pyhrf/pyhrf
def load_regnames(spmMatFile):
    d = loadmat(spmMatFile)
    spm = d["SPM"]
    return [s[0] for s in spm["xX"][0, 0]["name"][0, 0][0]]
示例#16
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文件: spmio.py 项目: pyhrf/pyhrf
def load_scalefactor_from_mat(spmMatFile):
    d = loadmat(spmMatFile)
    spm = d["SPM"]
    return float(get_field(get_field(spm, "xGX")[0][0], "gSF")[0][0][0][0])
示例#17
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文件: spmio.py 项目: ainafp/pyhrf
def load_regnames(spmMatFile):
    d = loadmat(spmMatFile)
    spm = d['SPM']
    return [s[0] for s in spm['xX'][0,0]['name'][0,0][0]]
示例#18
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文件: toolsTest.py 项目: ainafp/pyhrf
 def testOnSpmMat(self):
     spmFile = '/export/TMP/thomas/Data/Localizer/bru2698/functional/fMRI/'\
               'spm_analysis/SPM.mat'
     if os.path.exists(spmFile):
         from scipy.io.mio import loadmat
         spm = loadmat(spmFile)
示例#19
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 def testOnSpmMat(self):
     spmFile = '/export/TMP/thomas/Data/Localizer/bru2698/functional/fMRI/'\
               'spm_analysis/SPM.mat'
     if os.path.exists(spmFile):
         from scipy.io.mio import loadmat
         spm = loadmat(spmFile)
示例#20
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def loadOnsets(spmMatFile):
    d = loadmat(spmMatFile)
    spm = d['SPM']
    return get_onsets_from_spm_dict(spm)
示例#21
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def load_paradigm_from_mat(spmMatFile):
    d = loadmat(spmMatFile)
    spm = d['SPM']
    return (get_onsets_from_spm_dict(spm), get_tr_from_spm_dict(spm))
示例#22
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文件: spmio.py 项目: Solvi/pyhrf
def loadOnsets(spmMatFile):
    d = loadmat(spmMatFile)
    spm = d['SPM']
    
    return get_onsets_from_spm_dict(spm)
示例#23
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from os.path import exists

if len(argv) != 6:
    print "usage: %s DataDir QueueType BatchSize WriteOutData(yes/no) Timeout"%(argv[0])
    exit(1)

datadir = argv[1]
queue = argv[2]
batch_size = int(argv[3])
write_data = argv[4]
timeout = int(argv[5])

CPCluster=path[0]

# Load Batch_data and figure out the sets that need running
batch_info = loadmat("%(datadir)s/Batch_data.mat"%(locals()))
num_sets = batch_info['handles'].Current.NumberOfImageSets

# Loop over batches, check status file, print out commands for those that need it
for start in range(1, num_sets + 1, batch_size):
    end = start + batch_size - 1
    if end > num_sets:
        end = num_sets
    status_file_name = "%(datadir)s/status/Batch_%(start)d_to_%(end)d_DONE.mat"%(locals())
    if not exists(status_file_name):
        print "bsub -q %(queue)s -o %(datadir)s/txt_output/%(start)s_to_%(end)s.txt %(CPCluster)s/CPCluster.py %(datadir)s/Batch_data.mat %(start)s %(end)s %(datadir)s/status Batch_ %(write_data)s %(timeout)d"%(locals())



#  for i in `; do
#      echo bsub -q $QueueType -o ${BatchTxtOutputDir}/${i}.txt $CPCluster/CPCluster.sh ${BatchDataDir}/${BatchPrefix}data.mat $i $BatchStatusDir $BatchPrefix
示例#24
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     my_batch = {
         "email":         form_data["email"].value,
         "queue":         form_data["queue"].value,
         "data_dir":      form_data["data_dir"].value,
         "write_data":    (form_data["write_data"].value.upper()=="Y" and 1) or 0,
         "batch_size":    int(form_data["batch_size"].value),
         "timeout":       float(form_data["timeout"].value),
         "cpcluster":     CPCluster,
         "batch_file":    batch_file
         }
     error = CheckParameters(my_batch)
     if error:
         exception = RuntimeError()
         exception.message = error
         raise exception
     batch_info = loadmat(batch_file)
     my_batch["num_sets"] = batch_info['handles'].Current.NumberOfImageSets
     runs = PartitionBatches(my_batch)
     batch_id = RunBatch.CreateBatchRun(my_batch)
     results = RunBatch.RunAll(batch_id)
     text=[]
     text.append("<html>")
     text.append("<head><title>Batch # %d</title>"%(batch_id))
     text.append("<style type='text/css'>")
     text.append("""
 table {
     border-spacing: 0px;
     border-collapse: collapse;
 }
 td {
     text-align: left;