diff options
Diffstat (limited to 'examples/viewer3DVolume.py')
| -rw-r--r-- | examples/viewer3DVolume.py | 118 |
1 files changed, 75 insertions, 43 deletions
diff --git a/examples/viewer3DVolume.py b/examples/viewer3DVolume.py index 2193402..74ea27a 100644 --- a/examples/viewer3DVolume.py +++ b/examples/viewer3DVolume.py @@ -1,4 +1,3 @@ -# coding: utf-8 # /*########################################################################## # # Copyright (c) 2016-2020 European Synchrotron Radiation Facility @@ -29,8 +28,6 @@ an interactive cutting plane. It can also be started without providing a file. """ -from __future__ import absolute_import, division, unicode_literals - __authors__ = ["T. Vincent"] __license__ = "MIT" __date__ = "05/01/2017" @@ -54,6 +51,7 @@ _logger = logging.getLogger(__name__) import h5py + def load(filename): """Load 3D scalar field from file. @@ -63,35 +61,33 @@ def load(filename): and path in file for hdf5 file :return: numpy.ndarray with 3 dimensions. """ - if not os.path.isfile(filename.split('::')[0]): - raise IOError('No input file: %s' % filename) + if not os.path.isfile(filename.split("::")[0]): + raise IOError("No input file: %s" % filename) - if h5py.is_hdf5(filename.split('::')[0]): - if '::' not in filename: - raise ValueError( - 'HDF5 path not provided: Use <filename>::<path> format') + if h5py.is_hdf5(filename.split("::")[0]): + if "::" not in filename: + raise ValueError("HDF5 path not provided: Use <filename>::<path> format") - filename, path = filename.split('::') - path, indices = path.split('#')[0], path.split('#')[1:] + filename, path = filename.split("::") + path, indices = path.split("#")[0], path.split("#")[1:] - with h5py.File(filename, mode='r') as f: + with h5py.File(filename, mode="r") as f: data = f[path] # Loop through indices along first dimensions for index in indices: data = data[int(index)] - data = numpy.array(data, order='C', dtype='float32') + data = numpy.array(data, order="C", dtype="float32") else: # Try with numpy try: data = numpy.load(filename) except IOError: - raise IOError('Unsupported file format: %s' % filename) + raise IOError("Unsupported file format: %s" % filename) if data.ndim != 3: - raise RuntimeError( - 'Unsupported data set dimensions, only supports 3D datasets') + raise RuntimeError("Unsupported data set dimensions, only supports 3D datasets") return data @@ -110,32 +106,66 @@ def default_isolevel(data): # Parse input arguments -parser = argparse.ArgumentParser( - description=__doc__) +parser = argparse.ArgumentParser(description=__doc__) parser.add_argument( - '-l', '--level', nargs='?', type=float, default=float('nan'), - help="The value at which to generate the iso-surface") + "-l", + "--level", + nargs="?", + type=float, + default=float("nan"), + help="The value at which to generate the iso-surface", +) parser.add_argument( - '-sx', '--xscale', nargs='?', type=float, default=1., - help="The scale of the data on the X axis") + "-sx", + "--xscale", + nargs="?", + type=float, + default=1.0, + help="The scale of the data on the X axis", +) parser.add_argument( - '-sy', '--yscale', nargs='?', type=float, default=1., - help="The scale of the data on the Y axis") + "-sy", + "--yscale", + nargs="?", + type=float, + default=1.0, + help="The scale of the data on the Y axis", +) parser.add_argument( - '-sz', '--zscale', nargs='?', type=float, default=1., - help="The scale of the data on the Z axis") + "-sz", + "--zscale", + nargs="?", + type=float, + default=1.0, + help="The scale of the data on the Z axis", +) parser.add_argument( - '-ox', '--xoffset', nargs='?', type=float, default=0., - help="The offset of the data on the X axis") + "-ox", + "--xoffset", + nargs="?", + type=float, + default=0.0, + help="The offset of the data on the X axis", +) parser.add_argument( - '-oy', '--yoffset', nargs='?', type=float, default=0., - help="The offset of the data on the Y axis") + "-oy", + "--yoffset", + nargs="?", + type=float, + default=0.0, + help="The offset of the data on the Y axis", +) parser.add_argument( - '-oz', '--zoffset', nargs='?', type=float, default=0., - help="The offset of the data on the Z axis") + "-oz", + "--zoffset", + nargs="?", + type=float, + default=0.0, + help="The offset of the data on the Z axis", +) parser.add_argument( - 'filename', - nargs='?', + "filename", + nargs="?", default=None, help="""Filename to open. @@ -149,7 +179,8 @@ parser.add_argument( <filename>::<path_in_file>#<1st_dim_index>...#<n-3th_dim_index> E.g.: data.h5::/data_5D#1#1 - """) + """, +) args = parser.parse_args(args=sys.argv[1:]) # Start GUI @@ -164,18 +195,19 @@ treeView.setSfView(window) # Attach the parameter tree to the view # Add the parameter tree to the main window in a dock widget dock = qt.QDockWidget() -dock.setWindowTitle('Parameters') +dock.setWindowTitle("Parameters") dock.setWidget(treeView) window.addDockWidget(qt.Qt.RightDockWidgetArea, dock) # Load data from file if args.filename is not None: data = load(args.filename) - _logger.info('Data:\n\tShape: %s\n\tRange: [%f, %f]', - str(data.shape), data.min(), data.max()) + _logger.info( + "Data:\n\tShape: %s\n\tRange: [%f, %f]", str(data.shape), data.min(), data.max() + ) else: # Create dummy data - _logger.warning('Not data file provided, creating dummy data') + _logger.warning("Not data file provided, creating dummy data") coords = numpy.linspace(-10, 10, 64) z = coords.reshape(-1, 1, 1) y = coords.reshape(1, -1, 1) @@ -192,15 +224,15 @@ window.setScale(args.xscale, args.yscale, args.zscale) window.setTranslation(args.xoffset, args.yoffset, args.zoffset) # Set axes labels -window.setAxesLabels('X', 'Y', 'Z') +window.setAxesLabels("X", "Y", "Z") # Add an iso-surface if not numpy.isnan(args.level): # Add an iso-surface at the given iso-level - window.addIsosurface(args.level, '#FF0000FF') + window.addIsosurface(args.level, "#FF0000FF") else: # Add an iso-surface from a function - window.addIsosurface(default_isolevel, '#FF0000FF') + window.addIsosurface(default_isolevel, "#FF0000FF") window.show() -app.exec_() +app.exec() |