hdf5widget.py#
Sample code demonstrating silx.gui.hdf5 widgets:
#!/usr/bin/env python
# /*##########################################################################
#
# Copyright (c) 2016-2021 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# ###########################################################################*/
"""Qt Hdf5 widget examples"""
import html
import logging
import sys
import tempfile
import numpy
logging.basicConfig()
_logger = logging.getLogger("hdf5widget")
"""Module logger"""
try:
# it should be loaded before h5py
import hdf5plugin # noqa
except ImportError:
message = (
"Module 'hdf5plugin' is not installed. It supports some hdf5"
+ ' compressions. You can install it using "pip install hdf5plugin".'
)
_logger.warning(message)
import h5py
import silx.gui.hdf5
from silx.gui import qt
from silx.gui.data.DataViewerFrame import DataViewerFrame
from silx.gui.widgets.ThreadPoolPushButton import ThreadPoolPushButton
import fabio
_file_cache = {}
def str_attrs(str_list):
"""Return a numpy array of unicode strings"""
text_dtype = h5py.special_dtype(vlen=str)
return numpy.array(str_list, dtype=text_dtype)
def get_hdf5_with_all_types():
ID = "alltypes"
if ID in _file_cache:
return _file_cache[ID].name
tmp = tempfile.NamedTemporaryFile(prefix=ID + "_", suffix=".h5", delete=True)
tmp.file.close()
h5 = h5py.File(tmp.name, "w")
g = h5.create_group("arrays")
g.create_dataset("scalar", data=10)
g.create_dataset("list", data=numpy.arange(10))
base_image = numpy.arange(10**2).reshape(10, 10)
images = [
base_image,
base_image.T,
base_image.size - 1 - base_image,
base_image.size - 1 - base_image.T,
]
dtype = images[0].dtype
data = numpy.empty((10 * 10, 10, 10), dtype=dtype)
for i in range(10 * 10):
data[i] = images[i % 4]
data.shape = 10, 10, 10, 10
g.create_dataset("image", data=data[0, 0])
g.create_dataset("cube", data=data[0])
g.create_dataset("hypercube", data=data)
g = h5.create_group("dtypes")
g.create_dataset("int32", data=numpy.int32(10))
g.create_dataset("int64", data=numpy.int64(10))
g.create_dataset("float32", data=numpy.float32(10))
g.create_dataset("float64", data=numpy.float64(10))
g.create_dataset("string_", data=numpy.bytes_("Hi!"))
# g.create_dataset("string0",data=numpy.string0("Hi!\x00"))
g.create_dataset("bool", data=True)
g.create_dataset("bool2", data=False)
h5.close()
_file_cache[ID] = tmp
return tmp.name
def get_hdf5_with_all_links():
ID = "alllinks"
if ID in _file_cache:
return _file_cache[ID].name
tmp = tempfile.NamedTemporaryFile(prefix=ID + "_", suffix=".h5", delete=True)
tmp.file.close()
h5 = h5py.File(tmp.name, "w")
g = h5.create_group("group")
g.create_dataset("dataset", data=numpy.int64(10))
h5.create_dataset("dataset", data=numpy.int64(10))
h5["hard_link_to_group"] = h5["/group"]
h5["hard_link_to_dataset"] = h5["/dataset"]
h5["soft_link_to_group"] = h5py.SoftLink("/group")
h5["soft_link_to_dataset"] = h5py.SoftLink("/dataset")
h5["soft_link_to_nothing"] = h5py.SoftLink("/foo/bar/2000")
alltypes_filename = get_hdf5_with_all_types()
h5["external_link_to_group"] = h5py.ExternalLink(alltypes_filename, "/arrays")
h5["external_link_to_dataset"] = h5py.ExternalLink(
alltypes_filename, "/arrays/cube"
)
h5["external_link_to_nothing"] = h5py.ExternalLink(
alltypes_filename, "/foo/bar/2000"
)
h5["external_link_to_missing_file"] = h5py.ExternalLink("missing_file.h5", "/")
h5.close()
_file_cache[ID] = tmp
return tmp.name
def get_hdf5_with_1000_datasets():
ID = "dataset1000"
if ID in _file_cache:
return _file_cache[ID].name
tmp = tempfile.NamedTemporaryFile(prefix=ID + "_", suffix=".h5", delete=True)
tmp.file.close()
h5 = h5py.File(tmp.name, "w")
g = h5.create_group("group")
for i in range(1000):
g.create_dataset("dataset%i" % i, data=numpy.int64(10))
h5.close()
_file_cache[ID] = tmp
return tmp.name
def get_hdf5_with_10000_datasets():
ID = "dataset10000"
if ID in _file_cache:
return _file_cache[ID].name
tmp = tempfile.NamedTemporaryFile(prefix=ID + "_", suffix=".h5", delete=True)
tmp.file.close()
h5 = h5py.File(tmp.name, "w")
g = h5.create_group("group")
for i in range(10000):
g.create_dataset("dataset%i" % i, data=numpy.int64(10))
h5.close()
_file_cache[ID] = tmp
return tmp.name
def get_hdf5_with_100000_datasets():
ID = "dataset100000"
if ID in _file_cache:
return _file_cache[ID].name
tmp = tempfile.NamedTemporaryFile(prefix=ID + "_", suffix=".h5", delete=True)
tmp.file.close()
h5 = h5py.File(tmp.name, "w")
g = h5.create_group("group")
for i in range(100000):
g.create_dataset("dataset%i" % i, data=numpy.int64(10))
h5.close()
_file_cache[ID] = tmp
return tmp.name
def get_hdf5_with_recursive_links():
ID = "recursive_links"
if ID in _file_cache:
return _file_cache[ID].name
tmp = tempfile.NamedTemporaryFile(prefix=ID + "_", suffix=".h5", delete=True)
tmp.file.close()
h5 = h5py.File(tmp.name, "w")
g = h5.create_group("group")
g.create_dataset("dataset", data=numpy.int64(10))
h5.create_dataset("dataset", data=numpy.int64(10))
h5["hard_recursive_link"] = h5["/group"]
g["recursive"] = h5["hard_recursive_link"]
h5["hard_link_to_dataset"] = h5["/dataset"]
h5["soft_link_to_group"] = h5py.SoftLink("/group")
h5["soft_link_to_link"] = h5py.SoftLink("/soft_link_to_group")
h5["soft_link_to_itself"] = h5py.SoftLink("/soft_link_to_itself")
h5.close()
_file_cache[ID] = tmp
return tmp.name
def get_hdf5_with_external_recursive_links():
ID = "external_recursive_links"
if ID in _file_cache:
return _file_cache[ID][0].name
tmp1 = tempfile.NamedTemporaryFile(prefix=ID + "_", suffix=".h5", delete=True)
tmp1.file.close()
h5_1 = h5py.File(tmp1.name, "w")
tmp2 = tempfile.NamedTemporaryFile(prefix=ID + "_", suffix=".h5", delete=True)
tmp2.file.close()
h5_2 = h5py.File(tmp2.name, "w")
g = h5_1.create_group("group")
g.create_dataset("dataset", data=numpy.int64(10))
h5_1["soft_link_to_group"] = h5py.SoftLink("/group")
h5_1["external_link_to_link"] = h5py.ExternalLink(tmp2.name, "/soft_link_to_group")
h5_1["external_link_to_recursive_link"] = h5py.ExternalLink(
tmp2.name, "/external_link_to_recursive_link"
)
h5_1.close()
g = h5_2.create_group("group")
g.create_dataset("dataset", data=numpy.int64(10))
h5_2["soft_link_to_group"] = h5py.SoftLink("/group")
h5_2["external_link_to_link"] = h5py.ExternalLink(tmp1.name, "/soft_link_to_group")
h5_2["external_link_to_recursive_link"] = h5py.ExternalLink(
tmp1.name, "/external_link_to_recursive_link"
)
h5_2.close()
_file_cache[ID] = (tmp1, tmp2)
return tmp1.name
def get_hdf5_with_nxdata():
ID = "nxdata"
if ID in _file_cache:
return _file_cache[ID].name
tmp = tempfile.NamedTemporaryFile(prefix=ID + "_", suffix=".h5", delete=True)
tmp.file.close()
h5 = h5py.File(tmp.name, "w")
# SCALARS
g0d = h5.create_group("scalars")
g0d0 = g0d.create_group("0D_scalar")
g0d0.attrs["NX_class"] = "NXdata"
g0d0.attrs["signal"] = "scalar"
g0d0.create_dataset("scalar", data=10)
g0d1 = g0d.create_group("2D_scalars")
g0d1.attrs["NX_class"] = "NXdata"
g0d1.attrs["signal"] = "scalars"
ds = g0d1.create_dataset("scalars", data=numpy.arange(3 * 10).reshape((3, 10)))
ds.attrs["interpretation"] = "scalar"
g0d1 = g0d.create_group("4D_scalars")
g0d1.attrs["NX_class"] = "NXdata"
g0d1.attrs["signal"] = "scalars"
ds = g0d1.create_dataset(
"scalars", data=numpy.arange(2 * 2 * 3 * 10).reshape((2, 2, 3, 10))
)
ds.attrs["interpretation"] = "scalar"
# SPECTRA
g1d = h5.create_group("spectra")
g1d0 = g1d.create_group("1D_spectrum")
g1d0.attrs["NX_class"] = "NXdata"
g1d0.attrs["signal"] = "count"
g1d0.attrs["auxiliary_signals"] = str_attrs(["count.5", "count2"])
g1d0.attrs["axes"] = "energy_calib"
g1d0.attrs["uncertainties"] = str_attrs(["energy_errors"])
g1d0.create_dataset("count", data=numpy.arange(10))
g1d0.create_dataset("count.5", data=0.5 * numpy.arange(10))
d2 = g1d0.create_dataset("count2", data=2 * numpy.arange(10))
d2.attrs["long_name"] = "count multiplied by 2"
g1d0.create_dataset("energy_calib", data=(10, 5)) # 10 * idx + 5
g1d0.create_dataset("energy_errors", data=3.14 * numpy.random.rand(10))
g1d0.create_dataset("title", data="Title example provided as dataset")
g1d1 = g1d.create_group("2D_spectra")
g1d1.attrs["NX_class"] = "NXdata"
g1d1.attrs["signal"] = "counts"
ds = g1d1.create_dataset("counts", data=numpy.arange(3 * 10).reshape((3, 10)))
ds.attrs["interpretation"] = "spectrum"
g1d2 = g1d.create_group("4D_spectra")
g1d2.attrs["NX_class"] = "NXdata"
g1d2.attrs["signal"] = "counts"
g1d2.attrs["axes"] = str_attrs(["energy"])
ds = g1d2.create_dataset(
"counts", data=numpy.arange(2 * 2 * 3 * 10).reshape((2, 2, 3, 10))
)
ds.attrs["interpretation"] = "spectrum"
g1d2.create_dataset("errors", data=4.5 * numpy.random.rand(2, 2, 3, 10))
ds = g1d2.create_dataset(
"energy", data=5 + 10 * numpy.arange(15), shuffle=True, compression="gzip"
)
ds.attrs["long_name"] = "Calibrated energy"
ds.attrs["first_good"] = 3
ds.attrs["last_good"] = 12
g1d2.create_dataset("energy_errors", data=10 * numpy.random.rand(15))
# IMAGES
g2d = h5.create_group("images")
g2d0 = g2d.create_group("2D_regular_image")
g2d0.attrs["NX_class"] = "NXdata"
g2d0.attrs["signal"] = "image"
g2d0.attrs["auxiliary_signals"] = str_attrs(["image2", "image3"])
g2d0.attrs["axes"] = str_attrs(["rows_calib", "columns_coordinates"])
g2d0.attrs["title"] = "Title example provided as group attr"
g2d0.create_dataset("image", data=numpy.arange(4 * 6).reshape((4, 6)))
g2d0.create_dataset("image2", data=1 / (1.0 + numpy.arange(4 * 6).reshape((4, 6))))
ds = g2d0.create_dataset("image3", data=-numpy.arange(4 * 6).reshape((4, 6)))
ds.attrs["long_name"] = "3rd image (2nd auxiliary)"
ds = g2d0.create_dataset("rows_calib", data=(10, 5))
ds.attrs["long_name"] = "Calibrated Y"
g2d0.create_dataset("columns_coordinates", data=0.5 + 0.02 * numpy.arange(6))
g2d4 = g2d.create_group("RGBA_image")
g2d4.attrs["NX_class"] = "NXdata"
g2d4.attrs["signal"] = "image"
g2d4.attrs["auxiliary_signals"] = "squared image"
g2d4.attrs["axes"] = str_attrs(["rows_calib", "columns_coordinates"])
rgba_image = numpy.linspace(0, 1, num=7 * 8 * 3).reshape((7, 8, 3))
rgba_image[:, :, 1] = 1 - rgba_image[:, :, 1] # invert G channel to add some color
ds = g2d4.create_dataset("image", data=rgba_image)
ds.attrs["interpretation"] = "rgba-image"
ds = g2d4.create_dataset("squared image", data=rgba_image**2)
ds.attrs["interpretation"] = "rgba-image"
ds = g2d4.create_dataset("rows_calib", data=(10, 5))
ds.attrs["long_name"] = "Calibrated Y"
g2d4.create_dataset("columns_coordinates", data=0.5 + 0.02 * numpy.arange(8))
g2d1 = g2d.create_group("2D_irregular_data")
g2d1.attrs["NX_class"] = "NXdata"
g2d1.attrs["signal"] = "data"
g2d1.attrs["axes"] = str_attrs(["rows_coordinates", "columns_coordinates"])
g2d1.create_dataset("data", data=numpy.arange(64 * 128).reshape((64, 128)))
g2d1.create_dataset(
"rows_coordinates", data=numpy.arange(64) + numpy.random.rand(64)
)
g2d1.create_dataset(
"columns_coordinates", data=numpy.arange(128) + 2.5 * numpy.random.rand(128)
)
g2d2 = g2d.create_group("3D_images")
g2d2.attrs["NX_class"] = "NXdata"
g2d2.attrs["signal"] = "images"
ds = g2d2.create_dataset("images", data=numpy.arange(2 * 4 * 6).reshape((2, 4, 6)))
ds.attrs["interpretation"] = "image"
g2d3 = g2d.create_group("5D_images")
g2d3.attrs["NX_class"] = "NXdata"
g2d3.attrs["signal"] = "images"
g2d3.attrs["axes"] = str_attrs(["rows_coordinates", "columns_coordinates"])
ds = g2d3.create_dataset(
"images", data=numpy.arange(2 * 2 * 2 * 4 * 6).reshape((2, 2, 2, 4, 6))
)
ds.attrs["interpretation"] = "image"
g2d3.create_dataset("rows_coordinates", data=5 + 10 * numpy.arange(4))
g2d3.create_dataset("columns_coordinates", data=0.5 + 0.02 * numpy.arange(6))
# SCATTER
g = h5.create_group("scatters")
gd0 = g.create_group("x_y_scatter")
gd0.attrs["NX_class"] = "NXdata"
gd0.attrs["signal"] = "y"
gd0.attrs["axes"] = str_attrs(["x"])
gd0.attrs["title"] = "simple y = f(x) scatters cannot be distinguished from curves"
gd0.create_dataset("y", data=numpy.random.rand(128) - 0.5)
gd0.create_dataset("x", data=2 * numpy.random.rand(128))
gd0.create_dataset("x_errors", data=0.05 * numpy.random.rand(128))
gd0.create_dataset("errors", data=0.05 * numpy.random.rand(128))
gd1 = g.create_group("x_y_value_scatter")
gd1.attrs["NX_class"] = "NXdata"
gd1.attrs["signal"] = "values"
gd1.attrs["auxiliary_signals"] = str_attrs(["values.5", "values2"])
gd1.attrs["axes"] = str_attrs(["x", "y"])
gd1.attrs["title"] = "x, y, values scatter with asymmetric y_errors"
gd1.create_dataset("values", data=3.14 * numpy.random.rand(128))
gd1.create_dataset("values.5", data=0.5 * 3.14 * numpy.random.rand(128))
gd1.create_dataset("values2", data=2.0 * 3.14 * numpy.random.rand(128))
gd1.create_dataset("y", data=numpy.random.rand(128))
y_errors = [0.03 * numpy.random.rand(128), 0.04 * numpy.random.rand(128)]
gd1.create_dataset("y_errors", data=y_errors)
ds = gd1.create_dataset("x", data=2 * numpy.random.rand(128))
ds.attrs["long_name"] = "horizontal axis"
gd1.create_dataset("x_errors", data=0.02 * numpy.random.rand(128))
# NDIM > 3
g = h5.create_group("cubes")
gd0 = g.create_group("3D_cube")
gd0.attrs["NX_class"] = "NXdata"
gd0.attrs["signal"] = "cube"
gd0.attrs["axes"] = str_attrs(["img_idx", "rows_coordinates", "cols_coordinates"])
gd0.create_dataset("cube", data=numpy.arange(4 * 5 * 6).reshape((4, 5, 6)))
gd0.create_dataset("img_idx", data=numpy.arange(4))
gd0.create_dataset("rows_coordinates", data=0.1 * numpy.arange(5))
gd0.create_dataset("cols_coordinates", data=[0.2, 0.3]) # linear calibration
gd1 = g.create_group("5D")
gd1.attrs["NX_class"] = "NXdata"
gd1.attrs["signal"] = "hypercube"
gd1.create_dataset(
"hypercube", data=numpy.arange(2 * 3 * 4 * 5 * 6).reshape((2, 3, 4, 5, 6))
)
gd2 = g.create_group("3D_nonlinear_scaling")
gd2.attrs["NX_class"] = "NXdata"
gd2.attrs["signal"] = "cube"
gd2.attrs["axes"] = str_attrs(["img_idx", "rows_coordinates", "cols_coordinates"])
gd2.create_dataset("cube", data=numpy.arange(4 * 5 * 6).reshape((4, 5, 6)))
gd2.create_dataset("img_idx", data=numpy.array([2.0, -0.1, 8, 3.14]))
gd2.create_dataset("rows_coordinates", data=0.1 * numpy.arange(5))
gd2.create_dataset("cols_coordinates", data=[0.1, 0.6, 0.7, 8.0, 8.1, 8.2])
# invalid NXdata
g = h5.create_group("invalid")
g0 = g.create_group("invalid NXdata")
g0.attrs["NX_class"] = "NXdata"
g1 = g.create_group("invalid NXentry")
g1.attrs["NX_class"] = "NXentry"
g1.attrs["default"] = "missing NXdata group"
g2 = g.create_group("invalid NXroot")
g2.attrs["NX_class"] = "NXroot"
g2.attrs["default"] = "invalid NXentry in NXroot"
g20 = g2.create_group("invalid NXentry in NXroot")
g20.attrs["NX_class"] = "NXentry"
g20.attrs["default"] = "missing NXdata group"
h5.close()
_file_cache[ID] = tmp
return tmp.name
def get_edf_with_all_types():
ID = "alltypesedf"
if ID in _file_cache:
return _file_cache[ID].name
tmp = tempfile.NamedTemporaryFile(prefix=ID + "_", suffix=".edf", delete=True)
header = fabio.fabioimage.OrderedDict()
header["integer"] = "10"
header["float"] = "10.5"
header["string"] = "Hi!"
header["integer_list"] = "10 20 50"
header["float_list"] = "1.1 3.14 500.12"
header["motor_pos"] = "10 2.5 a1"
header["motor_mne"] = "integer_position float_position named_position"
data = numpy.array([[10, 50], [50, 10]])
fabiofile = fabio.edfimage.EdfImage(data, header)
fabiofile.write(tmp.name)
_file_cache[ID] = tmp
return tmp.name
def get_edf_with_100000_frames():
ID = "frame100000"
if ID in _file_cache:
return _file_cache[ID].name
tmp = tempfile.NamedTemporaryFile(prefix=ID + "_", suffix=".edf", delete=True)
fabiofile = None
for framre_id in range(100000):
data = numpy.array([[framre_id, 50], [50, 10]])
if fabiofile is None:
header = fabio.fabioimage.OrderedDict()
header["nb_frames"] = "100000"
fabiofile = fabio.edfimage.EdfImage(data, header)
else:
header = fabio.fabioimage.OrderedDict()
header["frame_nb"] = framre_id
fabiofile.append_frame(fabio.edfimage.Frame(data, header, framre_id))
fabiofile.write(tmp.name)
_file_cache[ID] = tmp
return tmp.name
class Hdf5TreeViewExample(qt.QMainWindow):
"""
This window show an example of use of a Hdf5TreeView.
The tree is initialized with a list of filenames. A panel allow to play
with internal property configuration of the widget, and a text screen
allow to display events.
"""
def __init__(self, filenames=None):
"""
:param files_: List of HDF5 or Spec files (pathes or
:class:`silx.io.spech5.SpecH5` or :class:`h5py.File`
instances)
"""
qt.QMainWindow.__init__(self)
self.setWindowTitle("Silx HDF5 widget example")
self.__asyncload = False
self.__treeview = silx.gui.hdf5.Hdf5TreeView(self)
"""Silx HDF5 TreeView"""
self.__text = qt.QTextEdit(self)
"""Widget displaying information"""
self.__dataViewer = DataViewerFrame(self)
vSpliter = qt.QSplitter(qt.Qt.Vertical)
vSpliter.addWidget(self.__dataViewer)
vSpliter.addWidget(self.__text)
vSpliter.setSizes([10, 0])
spliter = qt.QSplitter(self)
spliter.addWidget(self.__treeview)
spliter.addWidget(vSpliter)
spliter.setStretchFactor(1, 1)
main_panel = qt.QWidget(self)
layout = qt.QVBoxLayout()
layout.addWidget(spliter)
layout.addWidget(self.createTreeViewConfigurationPanel(self, self.__treeview))
layout.setStretchFactor(spliter, 1)
main_panel.setLayout(layout)
self.setCentralWidget(main_panel)
# append all files to the tree
for file_name in filenames:
self.__treeview.findHdf5TreeModel().appendFile(file_name)
self.__treeview.activated.connect(self.displayData)
self.__treeview.activated.connect(
lambda index: self.displayEvent("activated", index)
)
self.__treeview.clicked.connect(
lambda index: self.displayEvent("clicked", index)
)
self.__treeview.doubleClicked.connect(
lambda index: self.displayEvent("doubleClicked", index)
)
self.__treeview.entered.connect(
lambda index: self.displayEvent("entered", index)
)
self.__treeview.pressed.connect(
lambda index: self.displayEvent("pressed", index)
)
self.__treeview.addContextMenuCallback(self.customContextMenu)
# lambda function will never be called cause we store it as weakref
self.__treeview.addContextMenuCallback(lambda event: None)
# you have to store it first
self.__store_lambda = lambda event: self.closeAndSyncCustomContextMenu(event)
self.__treeview.addContextMenuCallback(self.__store_lambda)
def displayData(self):
"""Called to update the dataviewer with the selected data."""
selected = list(self.__treeview.selectedH5Nodes())
if len(selected) == 1:
# Update the viewer for a single selection
data = selected[0]
# data is a hdf5.H5Node object
# data.h5py_object is a Group/Dataset object (from h5py, spech5, fabioh5)
# The dataviewer can display both
self.__dataViewer.setData(data)
def displayEvent(self, eventName, index):
"""Called to log event in widget"""
def formatKey(name, value):
name, value = html.escape(str(name)), html.escape(str(value))
return "<li><b>%s</b>: %s</li>" % (name, value)
text = "<html>"
text += "<h1>Event</h1>"
text += "<ul>"
text += formatKey("name", eventName)
text += formatKey("index", type(index))
text += "</ul>"
text += "<h1>Selected HDF5 objects</h1>"
for h5_obj in self.__treeview.selectedH5Nodes():
text += "<h2>HDF5 object</h2>"
text += "<ul>"
text += formatKey("local_filename", h5_obj.local_file.filename)
text += formatKey("local_basename", h5_obj.local_basename)
text += formatKey("local_name", h5_obj.local_name)
text += formatKey("real_filename", h5_obj.file.filename)
text += formatKey("real_basename", h5_obj.basename)
text += formatKey("real_name", h5_obj.name)
text += formatKey("obj", h5_obj.ntype)
text += formatKey("dtype", getattr(h5_obj, "dtype", None))
text += formatKey("shape", getattr(h5_obj, "shape", None))
text += formatKey("attrs", getattr(h5_obj, "attrs", None))
if hasattr(h5_obj, "attrs"):
text += "<ul>"
if len(h5_obj.attrs) == 0:
text += "<li>empty</li>"
for key, value in h5_obj.attrs.items():
text += formatKey(key, value)
text += "</ul>"
text += "</ul>"
text += "</html>"
self.__text.setHtml(text)
def useAsyncLoad(self, useAsync):
self.__asyncload = useAsync
def __fileCreated(self, filename):
if self.__asyncload:
self.__treeview.findHdf5TreeModel().insertFileAsync(filename)
else:
self.__treeview.findHdf5TreeModel().insertFile(filename)
def customContextMenu(self, event):
"""Called to populate the context menu
:param silx.gui.hdf5.Hdf5ContextMenuEvent event: Event
containing expected information to populate the context menu
"""
selectedObjects = event.source().selectedH5Nodes()
menu = event.menu()
hasDataset = False
for obj in selectedObjects:
if obj.ntype is h5py.Dataset:
hasDataset = True
break
if not menu.isEmpty():
menu.addSeparator()
if hasDataset:
action = qt.QAction("Do something on the datasets", event.source())
menu.addAction(action)
def closeAndSyncCustomContextMenu(self, event):
"""Called to populate the context menu
:param silx.gui.hdf5.Hdf5ContextMenuEvent event: Event
containing expected information to populate the context menu
"""
selectedObjects = event.source().selectedH5Nodes()
menu = event.menu()
if not menu.isEmpty():
menu.addSeparator()
for obj in selectedObjects:
if obj.ntype is h5py.File:
action = qt.QAction("Remove %s" % obj.local_filename, event.source())
action.triggered.connect(
lambda: self.__treeview.findHdf5TreeModel().removeH5pyObject(
obj.h5py_object
)
)
menu.addAction(action)
action = qt.QAction(
"Synchronize %s" % obj.local_filename, event.source()
)
action.triggered.connect(
lambda: self.__treeview.findHdf5TreeModel().synchronizeH5pyObject(
obj.h5py_object
)
)
menu.addAction(action)
def __hdf5ComboChanged(self, index):
function = self.__hdf5Combo.itemData(index)
self.__createHdf5Button.setCallable(function)
def __edfComboChanged(self, index):
function = self.__edfCombo.itemData(index)
self.__createEdfButton.setCallable(function)
def createTreeViewConfigurationPanel(self, parent, treeview):
"""Create a configuration panel to allow to play with widget states"""
panel = qt.QWidget(parent)
panel.setLayout(qt.QHBoxLayout())
content = qt.QGroupBox("Create HDF5", panel)
content.setLayout(qt.QVBoxLayout())
panel.layout().addWidget(content)
combo = qt.QComboBox()
combo.addItem("Containing all types", get_hdf5_with_all_types)
combo.addItem("Containing all links", get_hdf5_with_all_links)
combo.addItem("Containing 1000 datasets", get_hdf5_with_1000_datasets)
combo.addItem("Containing 10000 datasets", get_hdf5_with_10000_datasets)
combo.addItem("Containing 100000 datasets", get_hdf5_with_100000_datasets)
combo.addItem("Containing recursive links", get_hdf5_with_recursive_links)
combo.addItem(
"Containing external recursive links",
get_hdf5_with_external_recursive_links,
)
combo.addItem("Containing NXdata groups", get_hdf5_with_nxdata)
combo.activated.connect(self.__hdf5ComboChanged)
content.layout().addWidget(combo)
button = ThreadPoolPushButton(content, text="Create")
button.setCallable(combo.itemData(combo.currentIndex()))
button.succeeded.connect(self.__fileCreated)
content.layout().addWidget(button)
self.__hdf5Combo = combo
self.__createHdf5Button = button
asyncload = qt.QCheckBox("Async load", content)
asyncload.setChecked(self.__asyncload)
asyncload.toggled.connect(lambda: self.useAsyncLoad(asyncload.isChecked()))
content.layout().addWidget(asyncload)
content.layout().addStretch(1)
content = qt.QGroupBox("Create EDF", panel)
content.setLayout(qt.QVBoxLayout())
panel.layout().addWidget(content)
combo = qt.QComboBox()
combo.addItem("Containing all types", get_edf_with_all_types)
combo.addItem("Containing 100000 datasets", get_edf_with_100000_frames)
combo.activated.connect(self.__edfComboChanged)
content.layout().addWidget(combo)
button = ThreadPoolPushButton(content, text="Create")
button.setCallable(combo.itemData(combo.currentIndex()))
button.succeeded.connect(self.__fileCreated)
content.layout().addWidget(button)
self.__edfCombo = combo
self.__createEdfButton = button
content.layout().addStretch(1)
option = qt.QGroupBox("Tree options", panel)
option.setLayout(qt.QVBoxLayout())
panel.layout().addWidget(option)
sorting = qt.QCheckBox("Enable sorting", option)
sorting.setChecked(
treeview.selectionMode() == qt.QAbstractItemView.MultiSelection
)
sorting.toggled.connect(lambda: treeview.setSortingEnabled(sorting.isChecked()))
option.layout().addWidget(sorting)
multiselection = qt.QCheckBox("Multi-selection", option)
multiselection.setChecked(
treeview.selectionMode() == qt.QAbstractItemView.MultiSelection
)
switch_selection = lambda: treeview.setSelectionMode(
qt.QAbstractItemView.MultiSelection
if multiselection.isChecked()
else qt.QAbstractItemView.SingleSelection
)
multiselection.toggled.connect(switch_selection)
option.layout().addWidget(multiselection)
filedrop = qt.QCheckBox("Drop external file", option)
filedrop.setChecked(treeview.findHdf5TreeModel().isFileDropEnabled())
filedrop.toggled.connect(
lambda: treeview.findHdf5TreeModel().setFileDropEnabled(
filedrop.isChecked()
)
)
option.layout().addWidget(filedrop)
filemove = qt.QCheckBox("Reorder files", option)
filemove.setChecked(treeview.findHdf5TreeModel().isFileMoveEnabled())
filemove.toggled.connect(
lambda: treeview.findHdf5TreeModel().setFileMoveEnabled(
filedrop.isChecked()
)
)
option.layout().addWidget(filemove)
option.layout().addStretch(1)
option = qt.QGroupBox("Header options", panel)
option.setLayout(qt.QVBoxLayout())
panel.layout().addWidget(option)
autosize = qt.QCheckBox("Auto-size headers", option)
autosize.setChecked(treeview.header().hasAutoResizeColumns())
autosize.toggled.connect(
lambda: treeview.header().setAutoResizeColumns(autosize.isChecked())
)
option.layout().addWidget(autosize)
columnpopup = qt.QCheckBox("Popup to hide/show columns", option)
columnpopup.setChecked(treeview.header().hasHideColumnsPopup())
columnpopup.toggled.connect(
lambda: treeview.header().setEnableHideColumnsPopup(columnpopup.isChecked())
)
option.layout().addWidget(columnpopup)
define_columns = qt.QComboBox()
define_columns.addItem(
"Default columns", treeview.findHdf5TreeModel().COLUMN_IDS
)
define_columns.addItem(
"Only name and Value",
[
treeview.findHdf5TreeModel().NAME_COLUMN,
treeview.findHdf5TreeModel().VALUE_COLUMN,
],
)
define_columns.activated.connect(
lambda index: treeview.header().setSections(define_columns.itemData(index))
)
option.layout().addWidget(define_columns)
option.layout().addStretch(1)
panel.layout().addStretch(1)
return panel
def main(filenames):
"""
:param filenames: list of file paths
"""
app = qt.QApplication([])
sys.excepthook = qt.exceptionHandler
window = Hdf5TreeViewExample(filenames)
window.show()
result = app.exec()
# remove ending warnings relative to QTimer
app.deleteLater()
sys.exit(result)
if __name__ == "__main__":
main(sys.argv[1:])