Formats for the ELDICO ED-1

newsfragments/682.feature

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+Add Bruker and miniCBF format readers for the ELDICO ED-1 electron diffractometer with DECTRIS QUADRO detector.

src/dxtbx/format/FormatBrukerED1.py

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+from __future__ import annotations
+
+from boost_adaptbx.boost.python import streambuf
+from scitbx import matrix
+from scitbx.array_family import flex
+
+from dxtbx import IncorrectFormatError
+from dxtbx.ext import (
+    is_big_endian,
+    read_uint8,
+    read_uint16,
+    read_uint16_bs,
+    read_uint32,
+    read_uint32_bs,
+)
+from dxtbx.format.FormatBruker import FormatBruker
+from dxtbx.model import SimplePxMmStrategy
+from dxtbx.model.beam import Probe
+
+
+class FormatBrukerED1(FormatBruker):
+    @staticmethod
+    def understand(image_file):
+
+        try:
+            header_lines = FormatBruker.read_header_lines(image_file)
+        except OSError:
+            return False
+
+        header_dic = FormatBruker.parse_header(header_lines)
+
+        dettype = header_dic.get("DETTYPE").upper()
+        if dettype is None:
+            return False
+
+        # ED-1 has a QUADRO detector (which is an EIGER)
+        if not ("EIGER" in dettype or "QUADRO" in dettype):
+            return False
+
+        # ED-1 energy is fixed at 160 keV
+        wavelength = float(header_dic["WAVELEN"].split()[0])
+        if round(wavelength, 3) != 0.029:
+            return False
+
+        return True
+
+    def _start(self):
+
+        try:
+            header_lines = FormatBruker.read_header_lines(self._image_file)
+        except OSError:
+            return False
+
+        self.header_dict = FormatBrukerED1.parse_header(header_lines)
+
+        # The ED-1 format can't currently use BrukerImage, for the same reason
+        # as for the Photon-II/III (hardcoded image size is one factor)
+        # https://github.com/cctbx/cctbx_project/issues/65
+        # from iotbx.detectors.bruker import BrukerImage
+        # self.detectorbase = BrukerImage(self._image_file)
+
+    def _goniometer(self):
+        # goniometer angles in ANGLES are 2-theta, omega, phi, chi (FIXED)
+        # AXIS indexes into this list to define the scan axis (in FORTRAN counting)
+        # START and RANGE define the start and step size for each image
+
+        _, omega, phi, chi = map(float, self.header_dict["ANGLES"].split())
+        scan_axis = ["NONE", "2THETA", "OMEGA", "PHI", "CHI", "X", "Y", "Z"]
+        scan_axis = scan_axis[int(self.header_dict["AXIS"])]
+        names = flex.std_string(("PHI", "CHI", "OMEGA"))
+        scan_axis = flex.first_index(names, scan_axis)
+        if scan_axis is None:
+            scan_axis = 2  # "OMEGA" default
+
+        # Axes here determined by trial and error to give the correct rotation
+        # axis for the ED-1 prototype, in which the CHI angle is 267°
+        axes = flex.vec3_double(((1, 0, 0), (0, 0, -1), (0, 1, 0)))
+        omega -= 180
+        angles = flex.double((phi, chi, omega))
+
+        # The ED-1 has a single-axis goniometer, but go through the multi-axis
+        # goniometer model to compose the axis.
+        g = self._goniometer_factory.make_multi_axis_goniometer(
+            axes, angles, names, scan_axis
+        )
+
+        # It is preferable to return a single axis goniometer, as this can be
+        # further optimised by dials.find_rotation_axis
+        return self._goniometer_factory.known_axis(g.get_rotation_axis())
+
+    def _calculate_gain(self, wavelength):
+        """The CCDPARM header item contains 5 items. For an X-ray detector
+        are described by:
+            1. readnoise
+            2. e/ADU
+            3. e/photon
+            4. bias
+            5. full scale
+        and the gain in ADU/X-ray is given by (e/photon) / (e/ADU).
+        For the ED-1 QUADRO, this should be 3.0 exactly, but some old files have
+        this inverted. In the case of exactly 1/3 gain, invert it back.
+        """
+        ccdparm = self.header_dict["CCDPARM"].split()
+        e_ADU = float(ccdparm[1])
+        e_photon = float(ccdparm[2])
+        if e_ADU == 0:
+            return 1.0
+        gain = e_photon / e_ADU
+        if gain == 1.0 / 3.0:
+            gain = 3.0
+        return gain
+
+    def _detector(self):
+        # goniometer angles in ANGLES are 2-theta, omega, phi, chi (FIXED)
+        two_theta = float(self.header_dict["ANGLES"].split()[0])
+
+        # Assume Bruker full_scale value means saturation
+        full_scale = float(self.header_dict["CCDPARM"].split()[-1])
+        min_trusted_value = 0
+
+        fast = matrix.col((1, 0, 0))
+        slow = matrix.col((0, -1, 0))
+        beam = matrix.col((0, 0, 1))
+        pixel_mm = 0.075
+        beam_pixel = [float(bp) for bp in self.header_dict["CENTER"].split()[:-3:-1]]
+        distance_mm = 10.0 * float(self.header_dict["DISTANC"].split()[1])
+        origin = (
+            -distance_mm * beam
+            - fast * pixel_mm * beam_pixel[1]
+            - slow * pixel_mm * beam_pixel[0]
+        )
+        # 2theta rotation appears to be around the slow axis
+        origin = origin.rotate_around_origin(slow, two_theta, deg=True)
+        fast = fast.rotate_around_origin(slow, two_theta, deg=True)
+        pixel_size = pixel_mm, pixel_mm
+        # ncols is nfast, nrows is nslow
+        image_size = (
+            int(self.header_dict["NCOLS"].split()[0]),
+            int(self.header_dict["NROWS"].split()[0]),
+        )
+
+        gain = self._calculate_gain(float(self.header_dict["WAVELEN"].split()[0]))
+        detector = self._detector_factory.complex(
+            "PAD",
+            origin.elems,
+            fast.elems,
+            slow.elems,
+            pixel_size,
+            image_size,
+            (min_trusted_value, full_scale),
+        )
+
+        # Here we set specifics, notably parallax correction and
+        # QE correction are effectively disabled by setting the simple
+        # pixel-to-millimetre strategy and a very high mu value.
+        for panel in detector:
+            panel.set_gain(gain)
+            panel.set_thickness(0.450)
+            panel.set_material("Si")
+            panel.set_px_mm_strategy(SimplePxMmStrategy())
+            panel.set_mu(1e10)
+
+        return detector
+
+    def _beam(self):
+        """Make unpolarized beam"""
+        wavelength = float(self.header_dict["WAVELEN"].split()[0])
+
+        return self._beam_factory.make_polarized_beam(
+            sample_to_source=(0.0, 0.0, 1.0),
+            wavelength=wavelength,
+            polarization=(0, 1, 0),
+            polarization_fraction=0.5,
+            probe=Probe.electron,
+        )
+
+    def _scan(self):
+
+        start = float(self.header_dict["START"].split()[0])
+        incr = float(self.header_dict["INCREME"].split()[0])
+        if incr < 0:
+            start *= -1
+            incr *= -1
+
+        return self._scan_factory.single_file(
+            filename=self._image_file,
+            exposure_times=1,
+            osc_start=start,
+            osc_width=incr,
+            epoch=None,
+        )
+
+    def get_raw_data(self):
+        """Get the pixel intensities (i.e. read the image and return as a
+        flex array of integers.)"""
+
+        # It is better to catch FORMAT 86 here and fail with a sensible error msg
+        # as soon as something is attempted with the image data rather than in
+        # the understand method. Otherwise the user gets FormatBruker reading the
+        # image improperly but without failing
+        if self.header_dict["FORMAT"] != "100":
+            raise NotImplementedError(
+                "Only FORMAT 100 images from the ED-1 are currently supported"
+            )
+
+        f = self.open_file(self._image_file, "rb")
+        header_size = int(self.header_dict["HDRBLKS"]) * 512
+        f.read(header_size)
+
+        if is_big_endian():
+            read_2b = read_uint16_bs
+            read_4b = read_uint32_bs
+        else:
+            read_2b = read_uint16
+            read_4b = read_uint32
+
+        # NPIXELB stores the number of bytes/pixel for the data and the underflow
+        # table. We expect 1 byte for underflows and either 2 or 1 byte per pixel
+        # for the data
+        npixelb = [int(e) for e in self.header_dict["NPIXELB"].split()]
+        assert npixelb[1] == 1
+
+        if npixelb[0] == 1:
+            read_data = read_uint8
+        elif npixelb[0] == 2:
+            read_data = read_2b
+        else:
+            raise IncorrectFormatError(
+                "{} bytes per pixel is not supported".format(npixelb[0])
+            )
+
+        nrows = int(self.header_dict["NROWS"].split()[0])
+        ncols = int(self.header_dict["NCOLS"].split()[0])
+
+        raw_data = read_data(streambuf(f), nrows * ncols)
+
+        image_size = (nrows, ncols)
+        raw_data.reshape(flex.grid(*image_size))
+
+        (num_underflows, num_2b_overflows, num_4b_overflows) = [
+            int(e) for e in self.header_dict["NOVERFL"].split()
+        ]
+
+        # read underflows
+        if num_underflows > 0:
+            # stored values are padded to a multiple of 16 bytes
+            nbytes = num_underflows + 15 & ~(15)
+            underflow_vals = read_uint8(streambuf(f), nbytes)[:num_underflows]
+        else:
+            underflow_vals = None
+
+        # handle 2 byte overflows
+        if num_2b_overflows > 0:
+            # stored values are padded to a multiple of 16 bytes
+            nbytes = num_2b_overflows * 2 + 15 & ~(15)
+            overflow_vals = read_2b(streambuf(f), nbytes // 2)[:num_2b_overflows]
+            overflow = flex.int(nrows * ncols, 0)
+            sel = (raw_data == 255).as_1d()
+            overflow.set_selected(sel, overflow_vals - 255)
+            overflow.reshape(flex.grid(*image_size))
+            raw_data += overflow
+
+        # handle 4 byte overflows
+        if num_4b_overflows > 0:
+            # stored values are padded to a multiple of 16 bytes
+            nbytes = num_4b_overflows * 4 + 15 & ~(15)
+            overflow_vals = read_4b(streambuf(f), nbytes // 4)[:num_4b_overflows]
+            overflow = flex.int(nrows * ncols, 0)
+            sel = (raw_data == 65535).as_1d()
+            overflow.set_selected(sel, overflow_vals - 65535)
+            overflow.reshape(flex.grid(*image_size))
+            raw_data += overflow
+
+        # handle underflows
+        if underflow_vals is not None:
+            sel = (raw_data == 0).as_1d()
+            underflow = flex.int(nrows * ncols, 0)
+            underflow.set_selected(sel, underflow_vals)
+            underflow.reshape(flex.grid(*image_size))
+            raw_data += underflow
+
+        # handle baseline. num_underflows == -1 means no baseline subtraction. See
+        # https://github.com/cctbx/cctbx_project/files/1262952/BISFrameFileFormats.zip
+        if num_underflows != -1:
+            num_exposures = [int(e) for e in self.header_dict["NEXP"].split()]
+            baseline = num_exposures[2]
+            raw_data += baseline
+
+        return raw_data