Merge pull request #1025 from vasole/itemsize

[XRF] Fast fit dynamically loaded integer data gave errors.

PyMca5/PyMcaPhysics/xrf/FastXRFLinearFit.py

@@ -736,7 +736,12 @@ def _fitLstSqReduced(self, data=None, sliceChan=None, mcaIndex=None,
     @staticmethod
     def _fitDtypeResult(data):
         if data.dtype not in [numpy.float32, numpy.float64]:
-            if data.itemsize < 5:
+            if hasattr(data, "itemsize"):
+                if data.itemsize < 5:
+                    return numpy.float32
+                else:
+                    return numpy.float64
+            elif (data.nbytes / data.size) < 5:
                 return numpy.float32
             else:
                 return numpy.float64

PyMca5/__init__.py

@@ -27,7 +27,7 @@
 __contact__ = "sole@esrf.fr"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__version__ = "5.8.8"
+__version__ = "5.8.9"
 
 import os
 import sys

PyMca5/tests/FastXRFLinearFitTest.py

@@ -0,0 +1,174 @@
+# /*##########################################################################
+#
+# The PyMca X-Ray Fluorescence Toolkit
+#
+# Copyright (c) 2023 European Synchrotron Radiation Facility
+#
+# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
+# the ESRF.
+#
+# 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.
+#
+#############################################################################*/
+__author__ = "V.A. Sole"
+__contact__ = "sole@esrf.eu"
+__license__ = "MIT"
+__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
+import unittest
+import sys
+import os
+import numpy
+import tempfile
+import shutil
+from PyMca5.tests import XrfData
+from PyMca5.PyMcaPhysics.xrf import FastXRFLinearFit
+from PyMca5.PyMcaPhysics.xrf.XRFBatchFitOutput import OutputBuffer
+
+try:
+    import h5py
+
+    HAS_H5PY = True
+except ImportError:
+    HAS_H5PY = False
+
+class testFastXRFLinearFit(unittest.TestCase):
+    _rtolLegacy = 1e-5
+
+    def setUp(self):
+        self.path = tempfile.mkdtemp(prefix="pymca")
+        super(testFastXRFLinearFit, self).setUp()
+
+    def tearDown(self):
+        shutil.rmtree(self.path)
+
+    @unittest.skipUnless(HAS_H5PY, "h5py not installed")
+    def testCommand(self):
+        from PyMca5.PyMcaIO import HDF5Stack1D
+
+        # generate the data
+        data, livetime = XrfData.generateXRFData()
+        configuration = XrfData.generateXRFConfig()
+        configuration["fit"]["stripalgorithm"] = 1
+
+        # create HDF5 file
+        fname = os.path.join(self.path, "FastXRF.h5")
+        h5 = h5py.File(fname, "w")
+        h5["/data"] = data
+        h5["/data_int32"] = (data * 1000).astype(numpy.int32)
+        h5.flush()
+        h5.close()
+
+        fastFit = FastXRFLinearFit.FastXRFLinearFit()
+        fastFit.setFitConfiguration(configuration)
+
+        outputDir = None
+        outputRoot = ""
+        fileEntry = ""
+        fileProcess = ""
+        refit = None
+        filepattern = None
+        begin = None
+        end = None
+        increment = None
+        backend = None
+        weight = 0
+        tif = 0
+        edf = 0
+        csv = 0
+        h5 = 1
+        dat = 0
+        concentrations = 0
+        diagnostics = 0
+        debug = 0
+        overwrite = 1
+        multipage = 0
+
+        outbuffer = OutputBuffer(
+            outputDir=outputDir,
+            outputRoot=outputRoot,
+            fileEntry=fileEntry,
+            fileProcess=fileProcess,
+            diagnostics=diagnostics,
+            tif=tif,
+            edf=edf,
+            csv=csv,
+            h5=h5,
+            dat=dat,
+            multipage=multipage,
+            overwrite=overwrite,
+        )
+
+        # test standard reading
+        scanlist = None
+        selection = {"y": "/data"}
+        dataStack = HDF5Stack1D.HDF5Stack1D([fname], selection, scanlist=scanlist)
+        with outbuffer.saveContext():
+            fastFit.fitMultipleSpectra(
+                y=dataStack,
+                weight=weight,
+                refit=refit,
+                concentrations=concentrations,
+                outbuffer=outbuffer,
+            )
+        # test dynamic reading
+        h5 = h5py.File(fname, "r")
+        with outbuffer.saveContext():
+            fastFit.fitMultipleSpectra(
+                y=h5["/data"],
+                weight=weight,
+                refit=refit,
+                concentrations=concentrations,
+                outbuffer=outbuffer,
+            )
+        # test dynamic reading of integer data
+        with outbuffer.saveContext():
+            fastFit.fitMultipleSpectra(
+                y=h5["/data_int32"],
+                weight=weight,
+                refit=refit,
+                concentrations=concentrations,
+                outbuffer=outbuffer,
+            )
+
+        h5.close()
+        h5 = None
+
+def getSuite(auto=True):
+    testSuite = unittest.TestSuite()
+    if auto:
+        testSuite.addTest(
+            unittest.TestLoader().loadTestsFromTestCase(testFastXRFLinearFit)
+        )
+    else:
+        # use a predefined order
+        testSuite.addTest(testPyMcaBatch("testCommand"))
+    return testSuite
+
+
+def test(auto=False):
+    return unittest.TextTestRunner(verbosity=2).run(getSuite(auto=auto))
+
+
+if __name__ == "__main__":
+    if len(sys.argv) > 1:
+        auto = False
+    else:
+        auto = True
+    result = test(auto)
+    sys.exit(not result.wasSuccessful())

PyMca5/tests/__init__.py

@@ -2,10 +2,10 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2019 European Synchrotron Radiation Facility
+# Copyright (c) 2004-2023 European Synchrotron Radiation Facility
 #
 # This file is part of the PyMca X-ray Fluorescence Toolkit developed at
-# the ESRF by the Software group.
+# the ESRF.
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -26,13 +26,14 @@
 # THE SOFTWARE.
 #
 #############################################################################*/
-__author__ = "V. Armando Sole - ESRF Data Analysis"
+__author__ = "V. Armando Sole"
 __contact__ = "sole@esrf.fr"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
 import os
 
 from PyMca5.tests.ConfigDictTest import test as testConfigDict
+from PyMca5.tests.DataTest import test as testDataTest
 from PyMca5.tests.EdfFileTest import test as testEdfFile
 from PyMca5.tests.ROIBatchTest import test as testROIBatch
 from PyMca5.tests.ElementsTest import test as testElements
@@ -44,6 +45,7 @@
 from PyMca5.tests.McaStackViewTest import test as testMcaStackView
 from PyMca5.tests.NexusUtilsTest import test as testNexusUtils
 from PyMca5.tests.StackInfoTest import test as testStackInfo
+from PyMca5.tests.FastXRFLinearFitTest import test as testFastXRFLinearFit
 
 def testAll():
     from PyMca5.tests.TestAll import main as testAll

changelog.txt

@@ -1,3 +1,8 @@
+VERSION 5.8.9
+-------------
+
+- FastXRF. Restore compatibility with dynamically loaded HDF5 data
+
 VERSION 5.8.8
 -------------