diff --git a/scm_confocal/visitech.py b/scm_confocal/visitech.py index db5b35c..65239ac 100644 --- a/scm_confocal/visitech.py +++ b/scm_confocal/visitech.py @@ -816,7 +816,8 @@ def __repr__(self): return "".format( self.filename,self.zsize,self.zstep,self.backsteps) - def load_data(self,indices=slice(None,None,None),dtype=np.uint16): + def load_data(self,indices=slice(None,None,None),dtype=np.uint16, + xslice=None,yslice=None): """ load images from datafile into 3D numpy array @@ -833,7 +834,14 @@ def load_data(self,indices=slice(None,None,None),dtype=np.uint16): if type(indices) == slice: indices = range(self.nf)[indices] - data = np.array(self.datafile[indices]) + if xslice is None and yslice is None: + data = np.array(self.datafile[indices]) + elif xslice is None: + data = np.array([self.datafile[i][yslice] for i in indices]) + elif yslice is None: + data = np.array([self.datafile[i][:,xslice] for i in indices]) + else: + data = np.array([self.datafile[i][yslice,xslice] for i in indices]) if not data.dtype == dtype: print('rescaling data to type',dtype) @@ -957,16 +965,6 @@ def load_stack(self,dim_range={},dtype=np.uint16,remove_backsteps=True, elif val==slice(None): dim_range.pop(key) - #warn for inefficient x and y trimming - if 'x-axis' in dim_range or 'y-axis' in dim_range: - print("[WARNING] scm_confocal.visitech_faststack.load_stack: "+ - "Loading only part of the data along dimensions 'x-axis' "+ - "and/or 'y-axis' not implemented. Data will be loaded fully"+ - " into memory before discarding values outside of the "+ - "slice range specified for the x-axis and/or y-axis. "+ - "Other axes for which a range is specified will still "+ - "be treated normally, avoiding unneccesary memory use.") - #remove values outside of dim_range from indices if 'time' in dim_range: indices = indices[dim_range['time']] @@ -983,18 +981,23 @@ def load_stack(self,dim_range={},dtype=np.uint16,remove_backsteps=True, # self.get_timestamps(load_stack_indices=True) self._stack_indices = indices + #add None arguments for x and y range if not slicing those + if not 'y-axis' in dim_range: + dim_range['y-axis'] = None + if not 'x-axis' in dim_range: + dim_range['x-axis'] = None + #load and reshape data - stack = self.load_data(indices=indices.ravel(),dtype=dtype) + stack = self.load_data( + indices=indices.ravel(), + dtype=dtype, + xslice=dim_range['x-axis'], + yslice=dim_range['y-axis'], + ) shape = (indices.shape[0],indices.shape[1],stack.shape[1], stack.shape[2]) stack = stack.reshape(shape) - #trim x and y axis - if 'y-axis' in dim_range: - stack = stack[:,:,dim_range['y-axis']] - if 'x-axis' in dim_range: - stack = stack[:,:,:,dim_range['x-axis']] - return stack def yield_stack(self,dim_range={},dtype=np.uint16,remove_backsteps=True,