Added I03 example grid scan

src/nexgen/beamlines/I03_2d_grid_scan_example.py

@@ -0,0 +1,198 @@
+"""
+Define beamline parameters for I03, Eiger detector and give an example of writing a gridscan.
+"""
+from contextlib import contextmanager
+import h5py
+import numpy as np
+import shutil
+
+from pathlib import Path
+import os
+
+from nexgen.nxs_write.NexusWriter import call_writers, ScanReader
+from nexgen.nxs_write.NXclassWriters import write_NXentry
+
+from nexgen.tools.VDS_tools import image_vds_writer
+
+
+source = {
+    "name": "Diamond Light Source",
+    "short_name": "DLS",
+    "type": "Synchrotron X-ray Source",
+    "beamline_name": "I03",
+}
+
+
+# fmt: off
+goniometer_axes = {
+    "axes": ["omega", "sam_z", "sam_y", "sam_x", "chi", "phi"],
+    "depends": [".", "omega", "sam_z", "sam_y", "sam_x", "chi"],
+    "vectors": [
+        -1, 0.0, 0.0,
+        0.0, 0.0, 1.0,
+        0.0, 1.0, 0.0,
+        1.0, 0.0, 0.0,
+        0.006, -0.0264, 0.9996
+        -1, -0.0025, -0.0056,
+    ],
+    "types": [
+        "rotation",
+        "translation",
+        "translation",
+        "translation",
+        "rotation",
+        "rotation",
+    ],
+    "units": ["deg", "mm", "mm", "mm", "deg", "deg"],
+    "offsets": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+    "starts": [150.0, 0.0, 186.5867, 420.9968, 0.0, 0.0],
+    "ends": [150.0, 0.0, 366.5867, 1040.9968, 0.0, 0.0],
+    "increments": [0.0, 0.0, 18, 20, 0.0, 0.0],
+}
+# fmt: on
+
+eiger16M_params = {
+    "mode": "images",
+    "description": "Eiger 16M",
+    "detector_type": "Pixel",
+    "sensor_material": "Silicon",
+    "sensor_thickness": "4.5E-4",
+    "overload": 46051,
+    "underload": -1,  # Not sure of this
+    "pixel_size": ["0.075mm", "0.075mm"],
+    "flatfield": "flatfield",
+    "flatfield_applied": "_dectris/flatfield_correction_applied",
+    "pixel_mask": "mask",
+    "pixel_mask_applied": "_dectris/pixel_mask_applied",
+    "image_size": [2068, 2162],  # (fast, slow)
+    "axes": ["det_z"],
+    "depends": ["."],
+    "vectors": [0.0, 0.0, 1.0],
+    "types": ["translation"],
+    "units": ["mm"],
+    "starts": [391.228416716],
+    "ends": [391.228416716],
+    "increments": [0.0],
+    "bit_depth_readout": "_dectris/bit_depth_readout",
+    "detector_readout_time": "_dectris/detector_readout_time",
+    "threshold_energy": "_dectris/threshold_energy",
+    "software_version": "_dectris/software_version",
+    "serial_number": "_dectris/detector_number",
+    "beam_center": [1062.4015611483892, 1105.631937699275],
+    "exposure_time": 0.004,
+}
+
+dset_links = [
+    [
+        "pixel_mask",
+        "pixel_mask_applied",
+        "flatfield",
+        "flatfield_applied",
+        "threshold_energy",
+        "bit_depth_readout",
+        "detector_readout_time",
+        "serial_number",
+    ],
+    ["software_version"],
+]
+
+# Initialize dictionaries
+goniometer = goniometer_axes
+detector = eiger16M_params
+module = {
+    "fast_axis": [-1.0, 0.0, 0.0],
+    "slow_axis": [0.0, -1.0, 0.0],
+    "module_offset": "1",
+}
+beam = {"wavelength": 0.976253543307, "flux": 9.475216962184312e11}
+attenuator = {"transmission": 0.4997258186340332}
+
+TEST_FILENAME = "protk_1_1{}"
+TEST_IMAGE_DATA = TEST_FILENAME.format("_000001.h5")
+TEST_METAFILE = TEST_FILENAME.format("_meta.h5")
+TEST_EXPECTED_NEXUS_FILE = TEST_FILENAME.format(".nxs")
+
+
+@contextmanager
+def get_test_data(remove_after_run=False):
+    test_data_folder = Path(
+        "/dls/i03/data/2022/cm31105-1/xraycentring/TestProteinaseK/protk_1/"
+    )
+    this_folder = Path(os.path.dirname(os.path.realpath(__file__)))
+    files = []
+    files.append(
+        shutil.copy(test_data_folder / TEST_IMAGE_DATA, this_folder / TEST_IMAGE_DATA)
+    )
+    files.append(
+        shutil.copy(test_data_folder / TEST_METAFILE, this_folder / TEST_METAFILE)
+    )
+    files.append(
+        shutil.copy(
+            test_data_folder / TEST_EXPECTED_NEXUS_FILE,
+            this_folder / TEST_FILENAME.format("_expected.nxs"),
+        )
+    )
+    try:
+        yield
+    finally:
+        if remove_after_run:
+            [os.remove(f) for f in files]
+
+
+def example_nexus_file():
+    """
+    Creates an example nexus file that should closely match the expected file
+    """
+
+    # Get timestamps in the correct format
+    timestamps = (
+        "2022-01-19T11:23:50Z",
+        "2022-01-19T11:24:01Z",
+    )
+
+    osc_scan, trans_scan = ScanReader(goniometer, snaked=True)
+
+    containing_foler = Path(os.path.dirname(os.path.realpath(__file__)))
+    test_nexus_file = containing_foler / "protk_1_1_test.nxs"
+    image_data = [containing_foler / TEST_IMAGE_DATA]
+    metafile = containing_foler / TEST_METAFILE
+
+    if test_nexus_file.exists():
+        print("File exists")
+        os.remove(test_nexus_file)
+
+    with h5py.File(test_nexus_file, "x") as nxsfile:
+        nxentry = write_NXentry(nxsfile)
+
+        if timestamps[0]:
+            nxentry.create_dataset("start_time", data=np.string_(timestamps[0]))
+
+        call_writers(
+            nxsfile,
+            image_data,
+            "mcstas",
+            ("images", 320),
+            goniometer,
+            detector,
+            module,
+            source,
+            beam,
+            attenuator,
+            osc_scan,
+            trans_scan,
+            metafile=metafile,
+            link_list=dset_links,
+        )
+
+        # Write VDS
+        image_vds_writer(
+            nxsfile, (320, detector["image_size"][1], detector["image_size"][0])
+        )
+
+        if timestamps[1]:
+            nxentry.create_dataset("end_time", data=np.string_(timestamps[1]))
+
+
+if __name__ == "__main__":
+    with get_test_data(True):
+        example_nexus_file()