Merge branch 'main' into 591_XDS

src/fabio/app/eiger2cbf.py

@@ -37,7 +37,7 @@
 __author__ = "Jerome Kieffer"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
 __licence__ = "MIT"
-__date__ = "03/12/2021"
+__date__ = "07/10/2024"
 __status__ = "production"
 
 import logging
@@ -259,7 +259,7 @@ def convert_one(input_filename, options, start_at=0):
     if options.pilatus:
         shape = select_pilatus_detecor(shape)
 
-    pilatus_headers = cbfimage.PilatusHeader("Silicon sensor, thickness 0.001 m")
+    pilatus_headers = cbfimage.PilatusHeader()
     if isinstance(source, limaimage.LimaImage):
         # Populate the Pilatus header from the Lima
         entry_name = source.h5.attrs.get("default")
@@ -290,7 +290,27 @@ def convert_one(input_filename, options, start_at=0):
                         except Exception as e:
                             logger.warning("Error in searching for exposure time (%s): %s", type(e), e)
     elif isinstance(source, eigerimage.EigerImage):
-        raise NotImplementedError("Please implement Eiger detector data format parsing or at least open an issue")
+        entry_name = source.h5.attrs.get("default")
+        if entry_name:
+            entry = source.h5.get(entry_name)
+            try:
+                nxdetector = entry["instrument/detector"]
+            except:
+                logger.error("No detector definition in Eiger file, is this a master file ?")
+            else:
+                detector = "%s, S/N %s" % (nxdetector["description"][()].decode(),
+                                           nxdetector["detector_number"][()].decode())
+                pilatus_headers["Detector"] = detector
+                pilatus_headers["Pixel_size"] = (nxdetector["x_pixel_size"][()],
+                                                 nxdetector["y_pixel_size"][()])
+                pilatus_headers["Exposure_time"] = nxdetector["count_time"][()]
+                pilatus_headers["Exposure_period"] = nxdetector["frame_time"][()]
+                pilatus_headers["Wavelength"] = entry["instrument/beam/incident_wavelength"][()] 
+                pilatus_headers["Detector_distance"] = nxdetector["detector_distance"][()] 
+                pilatus_headers["Beam_xy"] = (nxdetector["beam_center_x"][()],
+                                              nxdetector["beam_center_y"][()])
+                pilatus_headers["sensor"] = (nxdetector["sensor_material"][()].decode(),
+                                              nxdetector["sensor_thickness"][()])
     else:
         raise NotImplementedError("Unsupported format: %s" % source.__class__.__name__)
 
@@ -307,6 +327,8 @@ def convert_one(input_filename, options, start_at=0):
         pilatus_headers["Alpha"] = options.alpha
     if options.kappa:
         pilatus_headers["Kappa"] = options.kappa
+    if "sensor" not in pilatus_headers:
+        pilatus_headers["sensor"] = ("Silicon", 0.001)
     formula = None
     destination = None
     if options.chi is not None:

src/fabio/app/eiger2crysalis.py

@@ -38,7 +38,7 @@
 __author__ = "Jerome Kieffer"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
 __licence__ = "MIT"
-__date__ = "15/03/2024"
+__date__ = "09/10/2024"
 __status__ = "production"
 
 FOOTER = """To import your files as a project:
@@ -275,7 +275,22 @@ def common_headers(self):
                 headers["dexposuretimeinsec"] = 1  # meaningfull value.
 
             elif isinstance(source, eigerimage.EigerImage):
-                raise NotImplementedError("Please implement Eiger detector data format parsing or at least open an issue")
+                entry_name = source.h5.attrs.get("default")
+                if entry_name is None:
+                    entry_name = "entry"
+                entry = source.h5.get(entry_name)
+                try:
+                    nxdetector = entry["instrument/detector"]
+                except:
+                    logger.error("No detector definition in Eiger file, is this a master file ?")
+                else:
+                    headers["drealpixelsizex"] = nxdetector["x_pixel_size"][()] * 1e3
+                    headers["drealpixelsizey"] = nxdetector["y_pixel_size"][()] * 1e3
+                    headers["dxorigininpix"] = nxdetector["beam_center_x"][()]
+                    headers["dyorigininpix"] = nxdetector["beam_center_y"][()]
+                    headers["ddistanceinmm"] = nxdetector["detector_distance"][()] * 1e3
+                    headers["dexposuretimeinsec"] = nxdetector["count_time"][()]
+                    wavelength = entry["instrument/beam/incident_wavelength"][()] 
             else:
                 raise NotImplementedError("Unsupported format: %s" % source.__class__.__name__)
         if self.mask is None:
@@ -324,7 +339,7 @@ def common_headers(self):
                 value = numexpr.NumExpr(self.options.omega)
                 self.scan_type = "omega"
             headers["dom_s"] = headers["dom_e"] = value
-
+        
         return headers
 
     def convert_one(self, input_filename, start_at=0):
@@ -453,13 +468,14 @@ def treat_mask(self, full=False):
             dend = self.headers["dph_s"](self.processed_frames)
             dphi = 0.0
             domega = self.headers["dom_s"]
-        else: #Omega-scan
+        elif self.scan_type=="omega":
             iscantype = xcaliburimage.SCAN_TYPE.Omega.value
             dstart = self.headers["dom_s"](0)
             dend = self.headers["dom_s"](self.processed_frames)
             dphi = self.headers["dph_s"]
             domega = 0.0
-
+        else:
+            raise RuntimeError("This program only supports Omega and Phi scans, please provide the scan type in the command-line. See the output of the `--help` options.")
         oscil = (dend-dstart)/self.processed_frames
         sweep = xcaliburimage.Sweep(0,
                                     iscantype,

src/fabio/cbfimage.py

@@ -38,7 +38,7 @@
 __author__ = "Jérôme Kieffer"
 __contact__ = "[email protected]"
 __license__ = "MIT"
-__date__ = "04/07/2023"
+__date__ = "07/10/2024"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
 
 import os
@@ -923,9 +923,12 @@ def clean_string(cls, input_string):
             i += 1
         return lines
 
-    def __init__(self, content, convention="PILATUS_1.2"):
+    def __init__(self, content=None, convention="PILATUS_1.2"):
         assert convention == "PILATUS_1.2"
-        self._dict = self._parse(content)
+        if content:
+            self._dict = self._parse(content)
+        else:
+            self._dict = OrderedDict()
 
     def __repr__(self):
         lines = []
@@ -973,3 +976,6 @@ def __setitem__(self, key, value):
 
     def __getitem__(self, key):
         return self._dict[key]
+
+    def __contains__(self, key):
+        return key in self._dict