deploy: 76b5242

docs/CNAME

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+manual.nexusformat.org

docs/SPM_domain_app_def/CNAME

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+manual.nexusformat.org

docs/SPM_domain_app_def/_downloads/0a877a94f6f32b982b9a0c74073f6f01/write_nexus_file2.py

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+import numpy as np
+from nexusformat.nexus import *
+
+
+def write_nexus_file(fname, image, md={}):
+    """
+    write the image to a NeXus HDF5 data file
+
+    Parameters
+    ----------
+    fname : str
+        name of the file (relative or absolute) to be written
+    image : numpy array
+        the image data
+    md : dictionary
+        key: value where value is something that can be written by h5py
+             (such as str, int, float, numpy array, ...)
+    """
+    nx = NXroot()
+    nx['/entry'] = NXentry(NXinstrument(NXdetector()))
+    nx['entry/instrument/detector/image'] = NXfield(image, units='counts',
+                                                    compression='gzip')
+    nx['entry/data'] = NXdata()
+    nx['entry/data'].makelink(nx['entry/instrument/detector/image'])
+    nx['entry/data'].nxsignal = nx['entry/data/image']
+
+    if len(md) > 0:
+        # /entry/instrument/metadata (optional, for metadata)
+        metadata = nx['/entry/instrument/metadata'] = NXcollection()
+        for k, v in md.items():
+            metadata[k] = v
+
+    nx.save(fname, 'w')
+
+
+if __name__ == "__main__":
+	"""demonstrate how to use this code"""
+	import epics
+	prefix = "13SIM1:"
+	img = epics.caget(prefix+"image1:ArrayData")
+	size_x = epics.caget(prefix+"cam1:ArraySizeX_RBV")
+	size_y = epics.caget(prefix+"cam1:ArraySizeY_RBV")
+	# edit the full image for just the binned data
+	img = img[:size_x*size_y].reshape((size_x, size_y))
+
+	extra_information = dict(
+		unique_id = epics.caget(prefix+"image1:UniqueId_RBV"),
+		size_x = size_x,
+		size_y = size_y,
+		detector_state = epics.caget(prefix+"cam1:DetectorState_RBV"),
+		bitcoin_value="15000",
+	)
+	write_nexus_file("example.h5", img, md=extra_information)

docs/SPM_domain_app_def/_downloads/0ff27da7c434704769b51d02fbf4db92/external_counts_structure.txt

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+  entry:NXentry
+    @NX_class = "NXentry"
+    instrument:NXinstrument
+      @NX_class = "NXinstrument"
+      detector:NXdetector
+        @NX_class = "NXdetector"
+        counts:NX_INT32[31] = [1037, 1318, 1704, '...', 1321]
+          @units = "counts"
+        two_theta:NX_FLOAT64[31] = [17.92608, 17.92591, 17.92575, '...', 17.92108]
+          @units = "degrees"
+          @file = "external_angles.hdf5"
+          @path = "/angles"

docs/SPM_domain_app_def/_downloads/1937642b9af657d29b9267f91b81136f/attributes.xml

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+<?xml version="1.0" standalone="no" ?>
+<!-- Attributes -->
+<Attributes
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:noNamespaceSchemaLocation="https://github.com/areaDetector/ADCore/blob/master/iocBoot/NDAttributes.xsd"
+    >
+    <Attribute name="AcquireTime"         type="EPICS_PV" source="13SIM1:cam1:AcquireTime"      dbrtype="DBR_NATIVE"  description="Camera acquire time"/>
+    <Attribute name="ImageCounter"        type="PARAM"    source="ARRAY_COUNTER"                datatype="INT"        description="Image counter"/>
+    <Attribute name="calc1_val"           type="EPICS_PV" source="prj:userCalc1.VAL"            datatype="DBR_NATIVE" description="some calculation result"/>
+    <Attribute name="calc2_val"           type="EPICS_PV" source="prj:userCalc2.VAL"            datatype="DBR_NATIVE" description="another calculation result"/>
+    <Attribute name="MaxSizeX"            type="PARAM"    source="MAX_SIZE_X"                   datatype="INT"        description="Detector X size"/>
+    <Attribute name="MaxSizeY"            type="PARAM"    source="MAX_SIZE_Y"                   datatype="INT"        description="Detector Y size"/>
+    <Attribute name="CameraModel"         type="PARAM"    source="MODEL"                        datatype="STRING"     description="Camera model"/>
+    <Attribute name="CameraManufacturer"  type="PARAM"    source="MANUFACTURER"                 datatype="STRING"     description="Camera manufacturer"/>
+</Attributes>

docs/SPM_domain_app_def/_downloads/2d54d9af02ee715da23fed8d858526ba/simple_example_write1.py

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+#!/usr/bin/env python
+"""
+Writes the simplest NeXus HDF5 file using h5py
+
+Uses method accepted at 2014NIAC
+according to the example from Figure 1.3
+in the Introduction chapter
+"""
+
+from pathlib import Path
+
+import numpy
+
+from nexusformat.nexus import NXdata, NXentry, NXfield, nxopen
+
+filename = str(Path(__file__).absolute().parent.parent / "simple_example.dat")
+buffer = numpy.loadtxt(filename).T
+tthData = buffer[0]
+countsData = numpy.asarray(buffer[1], "int32")
+
+with nxopen("simple_example_write1.hdf5", "w") as f:  # create the NeXus file
+    f["Scan"] = NXentry()
+    tth = NXfield(tthData, name="two_theta", units="degrees")
+    counts = NXfield(countsData, name="counts", units="counts")
+    f["Scan/data"] = NXdata(counts, tth)

docs/SPM_domain_app_def/_downloads/3211ba74a45c7be2ed8549b5f33c6187/simple_example_write1.py

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+#!/usr/bin/env python
+"""
+Writes the simplest NeXus HDF5 file using h5py
+
+Uses method accepted at 2014NIAC
+according to the example from Figure 1.3
+in the Introduction chapter
+"""
+
+from pathlib import Path
+import h5py
+import numpy
+
+filename = str(Path(__file__).absolute().parent.parent / "simple_example.dat")
+buffer = numpy.loadtxt(filename).T
+tthData = buffer[0]  # float[]
+countsData = numpy.asarray(buffer[1], "int32")  # int[]
+
+with h5py.File("simple_example_write1.hdf5", "w") as f:  # create the HDF5 NeXus file
+    # since this is a simple example, no attributes are used at this point
+
+    nxentry = f.create_group("Scan")
+    nxentry.attrs["NX_class"] = "NXentry"
+
+    nxdata = nxentry.create_group("data")
+    nxdata.attrs["NX_class"] = "NXdata"
+    nxdata.attrs["signal"] = "counts"
+    nxdata.attrs["axes"] = "two_theta"
+    nxdata.attrs["two_theta_indices"] = [
+        0,
+    ]
+
+    tth = nxdata.create_dataset("two_theta", data=tthData)
+    tth.attrs["units"] = "degrees"
+
+    counts = nxdata.create_dataset("counts", data=countsData)
+    counts.attrs["units"] = "counts"

docs/SPM_domain_app_def/_downloads/36b2d63db078aaa74a2c739feae5e837/h5link.m

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+function h5link(filename, from, to)
+%H5LINK Create link to an HDF5 dataset.
+%   H5LINK(FILENAME,SOURCE,TARGET) creates an HDF5 link from the
+%   dataset at location SOURCE to a dataset at location TARGET.  All
+%   intermediate groups in the path to target are created.
+%
+%   Example:  create a link from /hello/world to /goodbye/world
+%      h5create('myfile.h5','/hello/world',[100 200]);
+%      h5link('myfile.h5','/hello/world','/goodbye/world');
+%      hgdisp('myfile.h5');
+%
+%   See also: h5create, h5read, h5write, h5info, h5disp
+
+% split from and to into group/dataset
+idx = strfind(from,'/');
+from_path = from(1:idx(end)-1);
+from_data = from(idx(end)+1:end);
+idx = strfind(to,'/');
+to_path = to(1:idx(end)-1);
+to_data = to(idx(end)+1:end);
+
+% open the HDF file
+fid = H5F.open(filename,'H5F_ACC_RDWR','H5P_DEFAULT');
+
+% create target group if it doesn't already exist
+create_intermediate = H5P.create('H5P_LINK_CREATE');
+H5P.set_create_intermediate_group(create_intermediate, 1);
+try
+    H5G.create(fid,to_path,create_intermediate,'H5P_DEFAULT','H5P_DEFAULT');
+catch
+end
+H5P.close(create_intermediate);
+
+% open groups and create link
+from_id = H5G.open(fid, from_path);
+to_id = H5G.open(fid, to_path);
+H5L.create_hard(from_id, from_data, to_id, to_data, 'H5P_DEFAULT','H5P_DEFAULT');
+
+% close all
+H5G.close(from_id);
+H5G.close(to_id);
+H5F.close(fid);
+end

docs/SPM_domain_app_def/_downloads/3a18cf1e63a6e3f68fb400d21e68231d/simple_example_write1_structure.txt

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+  Scan:NXentry
+    @NX_class = "NXentry"
+    data:NXdata
+      @NX_class = "NXdata"
+      @axes = "two_theta"
+      @signal = "counts"
+      @two_theta_indices = [0]
+      counts:NX_INT32[31] = [1037, 1318, 1704, '...', 1321]
+        @units = "counts"
+      two_theta:NX_FLOAT64[31] = [17.92608, 17.92591, 17.92575, '...', 17.92108]
+        @units = "degrees"

docs/SPM_domain_app_def/_downloads/3b7dde73e3bfd8b7c7fe8278259ef911/simple_example_write2.py

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+#!/usr/bin/env python
+"""
+Writes a simple NeXus HDF5 file using h5py with links
+according to the example from Figure 2.1 in the Design chapter
+"""
+
+from pathlib import Path
+import h5py
+import numpy
+
+filename = str(Path(__file__).absolute().parent.parent / "simple_example.dat")
+buffer = numpy.loadtxt(filename).T
+tthData = buffer[0]  # float[]
+countsData = numpy.asarray(buffer[1], "int32")  # int[]
+
+with h5py.File("simple_example_write2.hdf5", "w") as f:  # create the HDF5 NeXus file
+    f.attrs["default"] = "entry"
+
+    nxentry = f.create_group("entry")
+    nxentry.attrs["NX_class"] = "NXentry"
+    nxentry.attrs["default"] = "data"
+
+    nxinstrument = nxentry.create_group("instrument")
+    nxinstrument.attrs["NX_class"] = "NXinstrument"
+
+    nxdetector = nxinstrument.create_group("detector")
+    nxdetector.attrs["NX_class"] = "NXdetector"
+
+    # store the data in the NXdetector group
+    ds_tth = nxdetector.create_dataset("two_theta", data=tthData)
+    ds_tth.attrs["units"] = "degrees"
+    ds_counts = nxdetector.create_dataset("counts", data=countsData)
+    ds_counts.attrs["units"] = "counts"
+
+    # create the NXdata group to define the default plot
+    nxdata = nxentry.create_group("data")
+    nxdata.attrs["NX_class"] = "NXdata"
+    nxdata.attrs["signal"] = "counts"
+    nxdata.attrs["axes"] = "two_theta"
+    nxdata.attrs["two_theta_indices"] = [
+        0,
+    ]
+
+    source_addr = "/entry/instrument/detector/two_theta"  # existing data
+    target_addr = "two_theta"  # new location
+    ds_tth.attrs["target"] = source_addr  # a NeXus API convention for links
+    nxdata[target_addr] = f[source_addr]  # hard link
+    # nxdata._id.link(source_addr, target_addr, h5py.h5g.LINK_HARD)
+
+    source_addr = "/entry/instrument/detector/counts"  # existing data
+    target_addr = "counts"  # new location
+    ds_counts.attrs["target"] = source_addr  # a NeXus API convention for links
+    nxdata[target_addr] = f[source_addr]  # hard link
+    # nxdata._id.link(source_addr, target_addr, h5py.h5g.LINK_HARD)

docs/SPM_domain_app_def/_downloads/416583d2a0aeeb16432d9ff7e762f9ac/reader_attributes_trail.py

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+from pathlib import Path
+import h5py
+
+filename = str(
+    Path(__file__).absolute().parent.parent
+    / "simple_example_basic"
+    / "simple_example_basic.nexus.hdf5"
+)
+with h5py.File(filename, "r") as nx:
+    # find the default NXentry group
+    nx_entry = nx[nx.attrs["default"]]
+    # find the default NXdata group
+    nx_data = nx_entry[nx_entry.attrs["default"]]
+    # find the signal field
+    signal = nx_data[nx_data.attrs["signal"]]
+    # find the axes field(s)
+    attr_axes = nx_data.attrs["axes"]
+    if isinstance(attr_axes, (set, tuple, list)):
+        #  but check that attr_axes only describes 1-D data
+        if len(attr_axes) == 1:
+            attr_axes = attr_axes[0]
+        else:
+            raise ValueError(f"expected 1-D data but @axes={attr_axes}")
+    axes = nx_data[attr_axes]
+
+    print(f"file: {nx.filename}")
+    print(f"signal: {signal.name}")
+    print(f"axes: {axes.name}")
+    print(f"{axes.name} {signal.name}")
+    for x, y in zip(axes, signal):
+        print(x, y)