def render(input_polydata, number_of_fibers=None, opacity=1, depth_peeling=False, scalar_bar=False, axes=False, scalar_range=None, data_mode="Cell", tube=True, colormap='jet', data_name=None, verbose=True):
""" Function for easy matlab-like use of the rendering
functionality.
Returns RenderPolyData object which can be used directly for more
functionality."""
if verbose:
print "<render.py> Initiating rendering."
if number_of_fibers is not None:
if verbose:
print "<render.py> Downsampling vtkPolyData:", number_of_fibers
# downsample if requested
input_polydata = filter.downsample(input_polydata, number_of_fibers, preserve_point_data=True, preserve_cell_data=True, verbose=verbose)
if data_name is not None:
if verbose:
print "<render.py> Visualizing data:", data_name
if data_mode == "Cell":
input_polydata.GetCellData().SetActiveScalars(data_name)
if data_mode == "Point":
input_polydata.GetPointData().SetActiveScalars(data_name)
ren = RenderPolyData()
ren.render_polydata(input_polydata, opacity=opacity, depth_peeling=depth_peeling, scalar_bar=scalar_bar, axes=axes, scalar_range=scalar_range, data_mode=data_mode, tube=tube, colormap=colormap, verbose=verbose)
if verbose:
print "<render.py> Render pipeline created."
return ren
def rdmat(fn, samprds=0):
fp = h5py.File(fn, 'r') # open the .mat / HDF5 formatted data
sampr = fp['craw']['adrate'][0][0] # sampling rate
print('fn:', fn, 'sampr:', sampr, 'samprds:', samprds)
dt = 1.0 / sampr # time-step in seconds
dat = fp['craw']['cnt'] # cnt record stores the electrophys data
npdat = np.zeros(dat.shape)
tmax = (
len(npdat) - 1.0
) * dt # use original sampling rate for tmax - otherwise shifts phase
dat.read_direct(
npdat
) # read it into memory; note that this LFP data usually stored in microVolt
npdat *= 0.001 # convert microVolt to milliVolt here
fp.close()
if samprds > 0.0: # resample the LFPs
dsfctr = sampr / samprds
dt = 1.0 / samprds
siglen = max((npdat.shape[0], npdat.shape[1]))
nchan = min((npdat.shape[0], npdat.shape[1]))
npds = [] # zeros((int(siglen/float(dsfctr)),nchan))
# print dsfctr, dt, siglen, nchan, samprds, ceil(int(siglen / float(dsfctr))), npds.shape
for i in range(nchan):
print('resampling channel', i)
npds.append(downsample(npdat[:, i], sampr, samprds))
npdat = np.array(npds)
npdat = npdat.T
sampr = samprds
tt = np.linspace(0, tmax, len(npdat)) # time in seconds
return sampr, npdat, dt, tt # npdat is LFP in units of milliVolt
def render(input_polydata,
number_of_fibers=None,
opacity=1,
depth_peeling=False,
scalar_bar=False,
axes=False,
scalar_range=None,
data_mode="Cell",
tube=True,
colormap='jet',
data_name=None,
verbose=True):
""" Function for easy matlab-like use of the rendering
functionality.
Returns RenderPolyData object which can be used directly for more
functionality."""
if verbose:
print "<render.py> Initiating rendering."
if number_of_fibers is not None:
if verbose:
print "<render.py> Downsampling vtkPolyData:", number_of_fibers
# downsample if requested
input_polydata = filter.downsample(input_polydata,
number_of_fibers,
preserve_point_data=True,
preserve_cell_data=True,
verbose=verbose)
if data_name is not None:
if verbose:
print "<render.py> Visualizing data:", data_name
if data_mode == "Cell":
input_polydata.GetCellData().SetActiveScalars(data_name)
if data_mode == "Point":
input_polydata.GetPointData().SetActiveScalars(data_name)
ren = RenderPolyData()
ren.render_polydata(input_polydata,
opacity=opacity,
depth_peeling=depth_peeling,
scalar_bar=scalar_bar,
axes=axes,
scalar_range=scalar_range,
data_mode=data_mode,
tube=tube,
colormap=colormap,
verbose=verbose)
if verbose:
print "<render.py> Render pipeline created."
return ren
def read_and_preprocess_polydata_directory(input_dir,
fiber_length,
number_of_fibers,
random_seed=None,
fiber_length_max=None):
""" Find and read all .vtk and .vtp files in the given directory
input_dir. Preprocess with fiber length threshold and downsample
to desired number of fibers."""
input_pd_fnames = list_vtk_files(input_dir)
num_pd = len(input_pd_fnames)
print "<io.py> ======================================="
print "<io.py> Reading vtk and vtp files from directory: ", input_dir
print "<io.py> Total number of files found: ", num_pd
print "<io.py> ======================================="
input_pds = list()
subject_ids = list()
sidx = 0
for fname in input_pd_fnames:
subject_id = os.path.splitext(os.path.basename(fname))[0]
subject_ids.append(subject_id)
print "<io.py> ", sidx + 1, "/", num_pd, subject_id, " Reading ", fname, "..."
pd = read_polydata(fname)
print "<io.py> ", sidx + 1, "/", num_pd, subject_id, " Input number of fibers:", pd.GetNumberOfLines(
)
pd2 = filter.preprocess(pd,
min_length_mm=fiber_length,
verbose=False,
max_length_mm=fiber_length_max)
print "<io.py> ", sidx + 1, "/", num_pd, subject_id, " Length threshold", fiber_length, "mm. Number of fibers retained:", pd2.GetNumberOfLines(
)
pd3 = filter.downsample(pd2,
number_of_fibers,
verbose=False,
random_seed=random_seed)
print "<io.py> ", sidx + 1, "/", num_pd, subject_id, " Downsample to", number_of_fibers, "fibers. Number of fibers retained:", pd3.GetNumberOfLines(
)
input_pds.append(pd3)
sidx += 1
print "<io.py> ======================================="
print "<io.py> ======================================="
print "<io.py> Done reading vtk and vtp files from directory: ", input_dir
print "<io.py> Total number of files read: ", len(input_pds)
print "<io.py> ======================================="
return input_pds, subject_ids
def render(input_polydata, number_of_fibers=None, opacity=1, depth_peeling=False, scalar_bar=False, axes=False, scalar_range=None, data_mode="Cell", tube=True, colormap='jet'):
""" Function for easy matlab-like use of the rendering
functionality.
Returns RenderPolyData object which can be used directly for more
functionality."""
print "<render.py> Initiating rendering."
if number_of_fibers is not None:
print "<render.py> Downsampling vtkPolyData:", number_of_fibers
# downsample if requested
input_polydata = filter.downsample(input_polydata, number_of_fibers)
ren = RenderPolyData()
ren.render_polydata(input_polydata, opacity=opacity, depth_peeling=depth_peeling, scalar_bar=scalar_bar, axes=axes, scalar_range=scalar_range, data_mode=data_mode, tube=tube, colormap=colormap)
print "<render.py> Render pipeline created."
return ren
def read_and_preprocess_polydata_directory(input_dir, fiber_length, number_of_fibers):
""" Find and read all .vtk and .vtp files in the given directory
input_dir. Preprocess with fiber length threshold and downsample
to desired number of fibers."""
input_pd_fnames = list_vtk_files(input_dir)
num_pd = len(input_pd_fnames)
print "<io.py> ======================================="
print "<io.py> Reading vtk and vtp files from directory: ", input_dir
print "<io.py> Total number of files found: ", num_pd
print "<io.py> ======================================="
input_pds = list()
subject_ids = list()
sidx = 0
for fname in input_pd_fnames:
subject_id = os.path.splitext(os.path.basename(fname))[0]
subject_ids.append(subject_id)
print "<io.py> ", sidx + 1, "/", num_pd, subject_id, " Reading ", fname, "..."
pd = read_polydata(fname)
print "<io.py> ", sidx + 1, "/", num_pd, subject_id, " Input number of fibers:", pd.GetNumberOfLines()
pd2 = filter.preprocess(pd, fiber_length)
print "<io.py> ", sidx + 1, "/", num_pd, subject_id, " Length threshold", fiber_length, "mm. Number of fibers retained:", pd2.GetNumberOfLines()
pd3 = filter.downsample(pd2, number_of_fibers)
print "<io.py> ", sidx + 1, "/", num_pd, subject_id, " Downsample to", number_of_fibers, "fibers. Number of fibers retained:", pd3.GetNumberOfLines()
input_pds.append(pd3)
sidx += 1
print "<io.py> ======================================="
print "<io.py> ======================================="
print "<io.py> Done reading vtk and vtp files from directory: ", input_dir
print "<io.py> Total number of files read: ", len(input_pds)
print "<io.py> ======================================="
return input_pds, subject_ids
