HDF5Exporter handling of ragged curves with tests (#1072)
* HDF5Exporter handles ragged curves by saving them into different datasets based on their names. * Add HDF5Exporter tests * Document HDF5Exporter * Fix tmp file path
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@ -116,9 +116,9 @@ jobs:
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conda install -c conda-forge $(qt.bindings) --yes
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conda install -c conda-forge $(qt.bindings) --yes
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fi
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fi
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echo "Installing remainder of dependencies"
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echo "Installing remainder of dependencies"
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conda install -c conda-forge numpy scipy six pyopengl --yes
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conda install -c conda-forge numpy scipy six pyopengl h5py --yes
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else
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else
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pip install $(qt.bindings) numpy scipy pyopengl six
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pip install $(qt.bindings) numpy scipy pyopengl six h5py
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fi
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fi
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echo ""
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echo ""
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pip install pytest pytest-xdist pytest-cov coverage
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pip install pytest pytest-xdist pytest-cov coverage
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@ -30,8 +30,13 @@ Export Formats
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for export.
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for export.
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* Printer - Exports to the operating system's printing service. This exporter is provided for completeness,
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* Printer - Exports to the operating system's printing service. This exporter is provided for completeness,
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but is not well supported due to problems with Qt's printing system.
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but is not well supported due to problems with Qt's printing system.
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* HDF5 - Exports data from a :class:`~pyqtgraph.PlotItem` to a HDF5 file if
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h5py_ is installed. This exporter supports :class:`~pyqtgraph.PlotItem`
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objects containing multiple curves, stacking the data into a single HDF5
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dataset based on the ``columnMode`` parameter. If data items aren't the same
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size, each one is given its own dataset.
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.. _h5py: https://www.h5py.org/
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Exporting from the API
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Exporting from the API
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----------------------
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----------------------
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@ -44,20 +44,27 @@ class HDF5Exporter(Exporter):
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data = []
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data = []
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appendAllX = self.params['columnMode'] == '(x,y) per plot'
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appendAllX = self.params['columnMode'] == '(x,y) per plot'
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#print dir(self.item.curves[0])
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# Check if the arrays are ragged
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tlen = 0
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len_first = len(self.item.curves[0].getData()[0]) if self.item.curves[0] else None
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for i, c in enumerate(self.item.curves):
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ragged = any(len(i.getData()[0]) != len_first for i in self.item.curves)
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d = c.getData()
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if i > 0 and len(d[0]) != tlen:
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raise ValueError ("HDF5 Export requires all curves in plot to have same length")
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if appendAllX or i == 0:
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data.append(d[0])
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tlen = len(d[0])
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data.append(d[1])
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if ragged:
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dgroup = fd.create_group(dsname)
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for i, c in enumerate(self.item.curves):
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d = c.getData()
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fdata = numpy.array([d[0], d[1]]).astype('double')
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cname = c.name() if c.name() is not None else str(i)
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dset = dgroup.create_dataset(cname, data=fdata)
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else:
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for i, c in enumerate(self.item.curves):
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d = c.getData()
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if appendAllX or i == 0:
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data.append(d[0])
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data.append(d[1])
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fdata = numpy.array(data).astype('double')
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dset = fd.create_dataset(dsname, data=fdata)
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fdata = numpy.array(data).astype('double')
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dset = fd.create_dataset(dsname, data=fdata)
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fd.close()
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fd.close()
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if HAVE_HDF5:
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if HAVE_HDF5:
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71
pyqtgraph/exporters/tests/test_hdf5.py
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71
pyqtgraph/exporters/tests/test_hdf5.py
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@ -0,0 +1,71 @@
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# -*- coding: utf-8 -*-
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import pytest
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import pyqtgraph as pg
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from pyqtgraph.exporters import HDF5Exporter
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import numpy as np
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from numpy.testing import assert_equal
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import h5py
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import os
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@pytest.fixture
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def tmp_h5(tmp_path):
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yield tmp_path / "data.h5"
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@pytest.mark.parametrize("combine", [False, True])
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def test_HDF5Exporter(tmp_h5, combine):
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# Basic test of functionality: multiple curves with shared x array. Tests
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# both options for stacking the data (columnMode).
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x = np.linspace(0, 1, 100)
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y1 = np.sin(x)
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y2 = np.cos(x)
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plt = pg.plot()
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plt.plot(x=x, y=y1)
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plt.plot(x=x, y=y2)
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ex = HDF5Exporter(plt.plotItem)
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if combine:
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ex.parameters()['columnMode'] = '(x,y,y,y) for all plots'
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ex.export(fileName=tmp_h5)
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with h5py.File(tmp_h5, 'r') as f:
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# should be a single dataset with the name of the exporter
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dset = f[ex.parameters()['Name']]
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assert isinstance(dset, h5py.Dataset)
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if combine:
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assert_equal(np.array([x, y1, y2]), dset)
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else:
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assert_equal(np.array([x, y1, x, y2]), dset)
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def test_HDF5Exporter_unequal_lengths(tmp_h5):
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# Test export with multiple curves of different size. The exporter should
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# detect this and create multiple hdf5 datasets under a group.
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x1 = np.linspace(0, 1, 10)
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y1 = np.sin(x1)
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x2 = np.linspace(0, 1, 100)
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y2 = np.cos(x2)
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plt = pg.plot()
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plt.plot(x=x1, y=y1, name='plot0')
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plt.plot(x=x2, y=y2)
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ex = HDF5Exporter(plt.plotItem)
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ex.export(fileName=tmp_h5)
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with h5py.File(tmp_h5, 'r') as f:
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# should be a group with the name of the exporter
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group = f[ex.parameters()['Name']]
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assert isinstance(group, h5py.Group)
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# should be a dataset under the group with the name of the PlotItem
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assert_equal(np.array([x1, y1]), group['plot0'])
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# should be a dataset under the group with a default name that's the
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# index of the curve in the PlotItem
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assert_equal(np.array([x2, y2]), group['1'])
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