Add Nonius Kappa CCD format module

newsfragments/741.feature

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+Add Nonius KappaCCD format.

src/dxtbx/format/FormatNoniusKappaCCD.py

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+from __future__ import annotations
+
+import math
+import os
+import re
+import sys
+import time
+
+from boost_adaptbx.boost.python import streambuf
+from scitbx.array_family import flex
+
+from dxtbx import IncorrectFormatError
+from dxtbx.ext import is_big_endian, read_uint16, read_uint16_bs
+from dxtbx.format.Format import Format
+
+
+class FormatNoniusKappaCCD(Format):
+    """A class for reading files produced by 1990s era Nonius Kappa CCD instruments."""
+
+    @staticmethod
+    def read_header_lines(image_path):
+        """
+        Adapted from Fabio KcdImage _readheader
+        """
+
+        hdr_lines = []
+        end_of_headers = False
+        linect = 0
+        with Format.open_file(image_path, "rb") as f:
+            while not end_of_headers:
+                one_line = f.readline()
+                linect += 1
+                try:
+                    one_line = one_line.decode("ASCII")
+                except UnicodeDecodeError:
+                    end_of_headers = True
+                else:
+                    if len(one_line) > 100:
+                        end_of_headers = True
+                if not end_of_headers:
+                    if one_line.strip() == "Binned mode":
+                        one_line = "Mode = Binned"
+                    if "=" not in one_line and linect > 1:
+                        end_of_headers = True
+                    if not end_of_headers:
+                        hdr_lines.append(one_line)
+
+        return hdr_lines
+
+    @staticmethod
+    def parse_header(header_lines):
+        header_dic = {}
+
+        for l in header_lines:
+            separator = l.find("=")
+            if separator == -1:
+                continue
+            k = l[:separator].strip()
+            v = l[separator + 1 :].strip()
+            if k in header_dic:
+                header_dic[k] = header_dic[k] + "\n" + v
+            else:
+                header_dic[k] = v
+
+        return header_dic
+
+    @staticmethod
+    def understand(image_file):
+        """
+        Look for characteristic character sequences in the
+        header.
+        """
+        try:
+            with Format.open_file(image_file, "rb") as fh:
+                tag = fh.read(1024).decode("latin-1", "replace")
+        except OSError:
+            return False
+        if tag[0:2] != "No":
+            return False
+        if re.search("^Kappa-support angle", tag, re.MULTILINE) is None:
+            return False
+        if re.search("^Binned mode", tag, re.MULTILINE) is None:
+            return False
+        if re.search("^Shutter = Closed", tag, re.MULTILINE) is not None:
+            return False  # ignore dark current measurement
+        return True
+
+    def __init__(self, image_file, **kwargs):
+        """Initialise the image structure from the given file."""
+
+        if not self.understand(image_file):
+            raise IncorrectFormatError(self, image_file)
+        super().__init__(str(image_file), **kwargs)
+
+    def _start(self):
+        self.headers = self.parse_header(self.read_header_lines(self._image_file))
+
+    def _goniometer(self):
+        """Return model for a kappa goniometer"""
+        alpha = float(self.headers["Kappa-support angle"])
+        omega = float(self.headers["Omega start"])
+        kappa = float(self.headers["Kappa start"])
+        phi = float(self.headers["Phi start"])
+        direction = "-z"  #
+
+        if "Phi scan range" in self.headers:
+            scan_axis = "phi"
+        else:
+            scan_axis = "omega"
+
+        return self._goniometer_factory.make_kappa_goniometer(
+            alpha, omega, kappa, phi, direction, scan_axis
+        )
+
+    def _detector(self):
+        """It appears that pixel size reported in the header does not
+        account for binning, which doubles the size in both dimensions."""
+
+        pix_fac = 0.001
+        if self.headers["Mode"] == "Binned":
+            pix_fac = 0.002
+
+        pixel_size = [
+            float(self.headers["pixel X-size (um)"]) * pix_fac,
+            float(self.headers["pixel Y-size (um)"]) * pix_fac,
+        ]
+
+        image_size = [
+            float(self.headers["X dimension"]),
+            float(self.headers["Y dimension"]),
+        ]
+
+        beam_centre = (
+            image_size[0] * pixel_size[0] * 0.5,
+            image_size[1] * pixel_size[1] * 0.5,
+        )
+
+        gain = self.headers.get("Detector gain (ADU/count)", "1.0")
+        gain = float(gain)
+
+        return self._detector_factory.two_theta(
+            sensor="CCD",
+            distance=float(self.headers["Dx start"]),
+            beam_centre=beam_centre,
+            fast_direction="+y",  # Increasing to the right
+            slow_direction="+x",  # Down, same as rotation axis
+            two_theta_direction="+x",  # Same sense as omega and phi
+            two_theta_angle=float(self.headers["Theta start"]) * 2.0,
+            pixel_size=pixel_size,
+            image_size=image_size,
+            gain=gain,
+            identifier=self.headers["Detector ID"],
+            trusted_range=(0.0, 131070.0),  # May readout UInt16 twice
+        )
+
+    def _beam(self):
+        """Return a simple model for a lab-based beam. As dxtbx
+        has no laboratory target model, take the weighted values
+        of the alpha1/alpha2 wavelengths."""
+
+        a1 = float(self.headers["Alpha1"])
+        a2 = float(self.headers["Alpha2"])
+        wt = float(self.headers["Alpha1/Alpha2 ratio"])
+        wavelength = (wt * a1 + a2) / (wt + 1.0)
+        direction = [0.0, 0.0, 1.0]
+        polarisation, pol_dir = self.get_beam_polarisation()
+        return self._beam_factory.complex(
+            sample_to_source=direction,
+            wavelength=wavelength,
+            polarization_plane_normal=pol_dir,
+            polarization_fraction=polarisation,
+        )
+
+    def _scan(self):
+        """All scan dates will be in the range 1969-2068 as per
+        Python strptime. Please retire your CCD before 2069."""
+
+        if "Phi scan range" in self.headers:
+            rotax = "Phi"
+        else:
+            rotax = "Omega"
+
+        osc_start = float(self.headers["%s start" % rotax])
+        osc_range = float(self.headers["%s scan range" % rotax])
+        exposure_time = float(self.headers["Exposure time"])
+
+        simpletime = self.headers["Date"]
+        epoch = time.mktime(time.strptime(simpletime, "%a %m/%d/%y    %I:%M:%S %p"))
+
+        return self._scan_factory.single_file(
+            self._image_file, exposure_time, osc_start, osc_range, epoch
+        )
+
+    def get_beam_polarisation(self):
+        """Polarisation for single reflection off graphite 002
+        monochromator as per manual. Hard-coded angles for Mo, Cu and
+        Ag targets."""
+
+        if self.headers["Target material"] == "MO":
+            two_theta = 12.2  # From manual
+        elif self.headers["Target material"] == "CU":
+            two_theta = 26.6  # From manual
+        elif self.headers["Target material"] == "AG":
+            two_theta = 9.62  # Calculated
+
+        # Assume an ideally imperfect monochromator, with the axis
+        # of rotation of the monochromator in the horizontal direction
+        # in a laboratory setup.
+
+        pol_frac = 1.0 / (1 + math.cos(two_theta * math.pi / 180) ** 2)
+        pol_dir = [0.0, 1.0, 0.0]
+        return pol_frac, pol_dir
+
+    def get_raw_data(self):
+        """Return raw data from a Nonius CCD frame."""
+
+        # Frame file contains a series of readouts, each pixel is
+        # an unsigned little-endian 16-bit integer
+
+        dim1 = int(self.headers["X dimension"])
+        dim2 = int(self.headers["Y dimension"])
+        nbReadOut = int(self.headers["Number of readouts"])
+        expected_size = dim1 * dim2 * 2 * nbReadOut
+
+        # Not clear if the image offset is present in the header,
+        # therefore we seek from the end of the file.
+
+        with self.open_file(self._image_file, "rb") as infile:
+            fileSize = os.stat(self._image_file)[6]
+            infile.seek(fileSize - expected_size, os.SEEK_SET)
+
+            for i in range(nbReadOut):
+                if is_big_endian():
+                    raw_data = read_uint16_bs(streambuf(infile), dim1 * dim2)
+                else:
+                    raw_data = read_uint16(streambuf(infile), dim1 * dim2)
+
+                if i == 0:
+                    data = raw_data
+                else:
+                    data += raw_data
+
+        data.reshape(flex.grid(dim2, dim1))
+        return data
+
+
+if __name__ == "__main__":
+    for arg in sys.argv[1:]:
+        print(FormatNoniusKappaCCD.understand(arg))