python类io()的实例源码

def load_mat_file(name, path, matname, load_zeros = False, prop_valid_set = .1, prop_test_set=0):

    x = scipy.io.loadmat(path + name)[matname]


    if sp.issparse(x): 
        if not load_zeros:
            idxs = x.nonzero()

            indexes = np.array(zip(idxs[0], np.zeros_like(idxs[0]), idxs[1]))
            np.random.shuffle(indexes)

            nb = indexes.shape[0]
            i_valid = int(nb - nb*prop_valid_set - nb * prop_test_set)
            i_test = i_valid + int( nb*prop_valid_set)

            train = Triplets_set(indexes[:i_valid,:], np.ones(i_valid))
            valid = Triplets_set(indexes[i_valid:i_test,:], np.ones(i_test - i_valid))
            test = Triplets_set(indexes[i_test:,:], np.ones(nb - i_test))


    return Experiment(name,train, valid, test, positives_only = True, compute_ranking_scores = True)

def saveParams(self, lap, hmodel, SS=None, **kwargs):
        ''' Save current model to disk
        '''
        if lap in self.SavedIters or self.task_output_path is None:
            return
        ElapsedTimeLogger.startEvent("io", "saveparams")
        self.SavedIters.add(lap)
        prefix = ModelWriter.makePrefixForLap(lap)
        with open(self.mkfile('snapshot_lap.txt'), 'a') as f:
            f.write('%.4f\n' % (lap))
        with open(self.mkfile('snapshot_elapsed_time_sec.txt'), 'a') as f:
            f.write('%.3f\n' % (self.get_elapsed_time()))
        if self.outputParams['doSaveFullModel']:
            ModelWriter.save_model(
                hmodel, self.task_output_path, prefix,
                doSavePriorInfo=np.allclose(lap, 0.0),
                doLinkBest=True,
                doSaveObsModel=self.outputParams['doSaveObsModel'])
        if self.outputParams['doSaveTopicModel']:
            ModelWriter.saveTopicModel(
                hmodel, SS, self.task_output_path, prefix, **kwargs)
        ElapsedTimeLogger.stopEvent("io", "saveparams")

def run_motif(type,cell,thresh_mode):

    warnings.filterwarnings("ignore")

    print "cross_validation_training"
    print "motif features used"

    # Read data
    filename = "./pairs_%s%s_motif.mat"%(str(type),str(cell))
    data = scipy.io.loadmat(filename)
    x = np.asmatrix(data['seq_m'])
    y = np.ravel(data['lab_m'])
    y[y<0]=0
    print "Positive: %d  Negative: %d" % (sum(y==1), sum(y==0))

    k_fold = 10
    if thresh_mode==0:
        k_fold1 = 0
    elif thresh_mode==1:
        k_fold1 = 1
    else:
        k_fold1 = 5
    metrics_vec, pred, predicted, features1 = parametered_cv(x,y,k_fold,k_fold1,serial)

    filename1 = "test_%s%s_motiflab.txt"%(str(type), str(cell))
    filename2 = "test_%s%s_motifprob.txt"%(str(type), str(cell))
    filename3 = "test_%s%s_motiffeature.txt"%(str(type), str(cell))
    np.savetxt(filename1, pred, fmt='%d %d %d', delimiter='\t')
    np.savetxt(filename2, predicted, fmt='%f %f', delimiter='\t')
    np.savetxt(filename3, features1, fmt='%d %f', delimiter='\t')
    filename4 = "test_%s%s_motifthresh2.txt"%(str(type), str(cell))
    np.savetxt(filename4, metrics_vec, fmt='%f %f %f %f %f', delimiter='\t')

# Cross validation for PEP-Integrate

def run_shuffle(word, num_features,k,type,cell,sel_num,thresh_mode):

    warnings.filterwarnings("ignore")

    word = int(word)
    num_features = int(num_features)
    k = int(k)
    sel_num = int(sel_num)  

    print "Loading motif data"
    filename = "./pairs_%s%s_motif.mat"%(str(type),str(cell))
    data = scipy.io.loadmat(filename)
    x1 = np.asarray(data['seq_m'])
    y = np.ravel(data['lab_m'])
    y[y<0]=0
    print "Positive: %d Negative: %d" % (sum(y==1), sum(y==0))

    serial3 = np.array(range(0,x1.shape[1]))
    print serial3.shape
    print "shuffle features..."
    random.shuffle(serial3)
    x = x1[:,serial3]   

    filename4 = "test_%s%s_motifidx_shuffle%d.txt"%(str(type), str(cell), sel_num)
    np.savetxt(filename4, np.array((range(0,x1.shape[1]),serial3)).T, fmt='%d %d', delimiter='\t')

    k_fold = 10
    if thresh_mode==0:
        k_fold1 = 0
    elif thresh_mode==1:
        k_fold1 = 1
    else:
        k_fold1 = 5
    metrics_vec, pred, predicted, features1 = parametered_cv(x,y,k_fold,k_fold1)

    filename1 = "test_%s%s_motiflab_shuffle%d.txt"%(str(type), str(cell), sel_num)
    filename2 = "test_%s%s_motifprob_shuffle%d.txt"%(str(type), str(cell), sel_num)
    filename3 = "test_%s%s_motiffeature_shuffle%d.txt"%(str(type), str(cell), sel_num)
    np.savetxt(filename1, pred, fmt='%d %d %d', delimiter='\t')
    np.savetxt(filename2, predicted, fmt='%f %f', delimiter='\t')
    np.savetxt(filename3, features1, fmt='%d %f', delimiter='\t')

def __init__(self, Brain_image_filename,Electrode_ElectrodeData_filename,Electrode_mat_filename,ElectrodeSignals,ElectrodeSignalDataName):
            self.im = Image.open(Brain_image_filename)
            self.syllableUnit = 0 
            self.Timestep =0

            self.ElectrodeSignals = scipy.io.loadmat(ElectrodeSignals)
            self.mat = scipy.io.loadmat(Electrode_mat_filename)
            self.connectivityData = scipy.io.loadmat(Electrode_ElectrodeData_filename)

            # Changes for artificial data 
            Data=scipy.io.loadmat(Electrode_ElectrodeData_filename)

            temp = Data['electrode']
            self.ElectrodeIds = temp[0]
            self.ElectodeData = Data['C']

            # Changes for RealData
            # self.ElectrodeIds = [i for i in range(len(self.ElectrodeSignals[ElectrodeSignalDataName][0]))]
            # self.ElectodeData = self.connectivityData['conData']

            self.syllable, self.timestep, self.N , self.N  = np.shape(self.ElectodeData)
            self.timestep = self.timestep - 1

            """ The variables names for the new connecivity matrices, 
        C == correlation matrix 
            syllable == 6 syllables
            time = mapping between electrodes
            electrode == 58 electrodes  
            """

def initialize_transformer(image_mean):
  shape = (10*16, 3, 227, 227)
  transformer = caffe.io.Transformer({'data': shape})
  channel_mean = np.zeros((3,227,227))
  for channel_index, mean_val in enumerate(image_mean):
    channel_mean[channel_index, ...] = mean_val
  transformer.set_mean('data', channel_mean)
  transformer.set_raw_scale('data', 255)
  transformer.set_channel_swap('data', (2, 1, 0))
  transformer.set_transpose('data', (2, 0, 1))
  #transformer.set_is_flow('data', is_flow)
  return transformer

def singleFrame_classify_video(signal, net, transformer, with_smoothing, classNamesCNN):
    batch_size = 1 
    input_images = []

    input_im = caffe.io.load_image(signal.replace(".wav",".png"))        
    input_images.append(input_im)
    os.remove(signal.replace(".wav",".png"))    
    #Initialize predictions matrix                
    output_predictions = np.zeros((len(input_images),2))
    output_classes = []
    #print [method for method in dir(net) if callable(getattr(net, method))]    

    for i in range(0,len(input_images)):        
        # print "Classifying Spectrogram: ",i+1         
        clip_input = input_images[i:min(i+batch_size, len(input_images))] #get every image -- batch_size==1
        clip_input = caffe.io.oversample(clip_input,[227,227]) #make it 227x227        
        caffe_in = np.zeros(np.array(clip_input.shape)[[0,3,1,2]], dtype=np.float32) #initialize input matrix
        for ix, inputs in enumerate(clip_input):
            caffe_in[ix] = transformer.preprocess('data',inputs) # transform input data appropriatelly and add to input matrix        
        net.blobs['data'].reshape(caffe_in.shape[0], caffe_in.shape[1], caffe_in.shape[2], caffe_in.shape[3]) #make input caffe readable        
        out = net.forward_all(data=caffe_in) #feed input to the network
        output_predictions[i:i+batch_size] = np.mean(out['probs'].reshape(10,caffe_in.shape[0]/10,2),0) #predict labels        

        #Store predicted Labels without smoothing        
        iMAX = output_predictions[i:i+batch_size].argmax(axis=1)[0]
        prediction = classNamesCNN[iMAX]
        output_classes.append(prediction)
        #print "Predicted Label for file -->  ", signal.upper() ,":",    prediction
    return output_classes, output_predictions

def savemat(file_name, mdict, oned_as="column", **kwargs):
    """MATLAB-format output routine that is compatible with SciPy 0.7's.

    0.7.2 (or .1?) added the oned_as keyword arg with 'column' as the default
    value. It issues a warning if this is not provided, stating that "This will
    change to 'row' in future versions."
    """
    import scipy.io
    try:
        return scipy.io.savemat(file_name, mdict, oned_as=oned_as, **kwargs)
    except TypeError:
        return scipy.io.savemat(file_name, mdict, **kwargs)

def _load_sbd_mask_annotations(self, index, gt_roidbs):
        """
        Load gt_masks information from SBD's additional data
        """
        if index % 1000 == 0:
            print '%d / %d' % (index, len(self._image_index))
        image_name = self._image_index[index]
        inst_file_name = os.path.join(self._data_path, 'inst', image_name + '.mat')
        gt_inst_mat = scipy.io.loadmat(inst_file_name)
        gt_inst_data = gt_inst_mat['GTinst']['Segmentation'][0][0]
        unique_inst = np.unique(gt_inst_data)
        background_ind = np.where(unique_inst == 0)[0]
        unique_inst = np.delete(unique_inst, background_ind)
        gt_roidb = gt_roidbs[index]
        cls_file_name = os.path.join(self._data_path, 'cls', image_name + '.mat')
        gt_cls_mat = scipy.io.loadmat(cls_file_name)
        gt_cls_data = gt_cls_mat['GTcls']['Segmentation'][0][0]
        gt_masks = []
        for ind, inst_mask in enumerate(unique_inst):
            box = gt_roidb['boxes'][ind]
            im_mask = (gt_inst_data == inst_mask)
            im_cls_mask = np.multiply(gt_cls_data, im_mask)
            unique_cls_inst = np.unique(im_cls_mask)
            background_ind = np.where(unique_cls_inst == 0)[0]
            unique_cls_inst = np.delete(unique_cls_inst, background_ind)
            assert len(unique_cls_inst) == 1
            assert unique_cls_inst[0] == gt_roidb['gt_classes'][ind]
            mask = im_mask[box[1]: box[3]+1, box[0]:box[2]+1]
            gt_masks.append(mask)

        # Also record the maximum dimension to create fixed dimension array when do forwarding
        mask_max_x = max(gt_masks[i].shape[1] for i in xrange(len(gt_masks)))
        mask_max_y = max(gt_masks[i].shape[0] for i in xrange(len(gt_masks)))
        return {
            'gt_masks': gt_masks,
            'mask_max': [mask_max_x, mask_max_y],
            'flipped': False
        }