Merge pull request #2419 from kif/diffmap

Diffmap

src/pyFAI/app/integrate.py

@@ -33,7 +33,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "14/02/2025"
+__date__ = "17/02/2025"
 __satus__ = "production"
 
 import sys

src/pyFAI/diffmap.py

@@ -31,7 +31,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "27/01/2025"
+__date__ = "19/02/2025"
 __status__ = "development"
 __docformat__ = 'restructuredtext'
 
@@ -53,6 +53,7 @@
 from . import version as PyFAI_VERSION, date as PyFAI_DATE
 from .integrator.load_engines import  PREFERED_METHODS_2D, PREFERED_METHODS_1D
 from .io import Nexus, get_isotime, h5py
+from .io.integration_config import WorkerConfig
 from .worker import Worker
 from .utils.decorators import deprecated, deprecated_warning
 
@@ -380,10 +381,13 @@ def parse(self, sysargv=None, with_config=False):
     def configure_worker(self, dico=None):
         """Configure the worker from the dictionary
 
-        :param dico: dictionary with the configuration
+        :param dico: dictionary/WorkerConfig with the configuration
         :return: worker
         """
+        if isinstance(dico, dict):
+            dico = WorkerConfig.from_dict(dico)
         self.worker.set_config(dico or self.poni)
+        self.init_shape(dico.shape)
 
     def makeHDF5(self, rewrite=False):
         """
@@ -439,7 +443,6 @@ def makeHDF5(self, rewrite=False):
         process_grp["offset"] = self.offset
         config = nxs.new_class(process_grp, "configuration", "NXnote")
         config["type"] = "text/json"
-        self.init_shape()
         worker_config = self.worker.get_config()
         config["data"] = json.dumps(worker_config, indent=2, separators=(",\r\n", ": "))
 
@@ -497,20 +500,25 @@ def makeHDF5(self, rewrite=False):
         self.dataset.attrs["title"] = self.nxdata_grp["map"].attrs["title"] = str(self)
         self.nxs = nxs
 
-    def init_shape(self):
+    def init_shape(self, shape=None):
         """Initialize the worker with the proper input shape
 
+        :param shape: enforce the shape to initialize to
         :return: shape of the individual frames
         """
-        # if shape of detector undefined: reading the first image to guess it
-        if self.ai.detector.shape:
-            shape = self.ai.detector.shape
-        else:
+        former_shape = self.worker.ai.detector.shape
+        try:
             with fabio.open(self.inputfiles[0]) as fimg:
-                shape = fimg.data.shape
-            self.worker.ai.shape = shape
-            self.worker._shape = shape
-        self.worker.output = "raw"
+                new_shape = fimg.data.shape
+        except:
+            new_shape = None
+        shape = new_shape or shape or former_shape
+        self.worker.ai.shape = shape
+        self.worker._shape = shape
+        print(f"reconfigure worker with shape {shape}")
+        self.worker.reconfig(shape, sync=True)
+        self.worker.output = "raw" #after reconfig !
+        self.worker.safe = False
         return shape
 
     def init_ai(self):
@@ -522,17 +530,12 @@ def init_ai(self):
             self.configure_worker(self.poni)
         if not self.nxdata_grp:
             self.makeHDF5(rewrite=False)
-        shape = self.init_shape()
-        data = numpy.empty(shape, dtype=numpy.float32)
         logger.info(f"Initialization of the Azimuthal Integrator using method {self.method}")
         # enforce initialization of azimuthal integrator
-        print(self.ai)
-        res = self.worker.process(data)
-        tth = res.radial
-        if self.dataset is None:
-            self.makeHDF5()
+        logger.info(f"Detector shape: {self.ai.detector.shape} mask shape {self.ai.detector.mask.shape}")
+        tth = self.worker.radial
 
-        if res.sigma is not None:
+        if self.worker.propagate_uncertainties:
             self.dataset_error = self.nxdata_grp.create_dataset("errors",
                                                                 shape=self.dataset.shape,
                                                                 dtype="float32",
@@ -542,16 +545,16 @@ def init_ai(self):
         space = self.unit.space
         unit = str(self.unit)[len(space) + 1:]
         if space not in self.nxdata_grp:
-            self.nxdata_grp[space] = tth
-            self.nxdata_grp[space].attrs["unit"] = unit
-            self.nxdata_grp[space].attrs["long_name"] = self.unit.label
-            self.nxdata_grp[space].attrs["interpretation"] = "scalar"
+            tthds = self.nxdata_grp.create_dataset(space, data=tth)
+            tthds.attrs["unit"] = unit
+            tthds.attrs["long_name"] = self.unit.label
+            tthds.attrs["interpretation"] = "scalar"
         if self.worker.do_2D():
-            self.nxdata_grp["azimuthal"] = res.azimuthal
-            self.nxdata_grp["azimuthal"].attrs["unit"] = "deg"
-            self.nxdata_grp["azimuthal"].attrs["interpretation"] = "scalar"
-            self.nxdata_grp["azimuthal"].attrs["axes"] = 1
-            azim = res.azimuthal
+            azimds = self.nxdata_grp.create_dataset("azimuthal", data=self.worker.azimuthal)
+            azimds.attrs["unit"] = "deg"
+            azimds.attrs["interpretation"] = "scalar"
+            azimds.attrs["axes"] = 1
+            azim = self.worker.azimuthal
             self.nxdata_grp[space].attrs["axes"] = 2
         else:
             self.nxdata_grp[space].attrs["axes"] = 1
@@ -672,10 +675,9 @@ def process(self):
             self.makeHDF5()
         self.init_ai()
         t0 = -time.perf_counter()
-        print(self.inputfiles)
         for f in self.inputfiles:
             self.process_one_file(f)
-        t0 -= time.perf_counter()
+        t0 += time.perf_counter()
         cnt = max(self._idx, 0) + 1
         print(f"Execution time for {cnt} frames: {t0:.3f} s; "
               f"Average execution time: {1000. * t0 / cnt:.1f} ms/img")

src/pyFAI/geometry/core.py

@@ -40,7 +40,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "31/01/2025"
+__date__ = "19/02/2025"
 __status__ = "production"
 __docformat__ = 'restructuredtext'
 
@@ -1357,24 +1357,32 @@ def load(self, filename):
         """
         Load the refined parameters from a file.
 
-        :param filename: name of the file to load. Can also be a JSON string with a dict or dict
-        :type filename: string
+        :param filename: name of the file to load. Can also be a JSON string with a dict or dict or geometry
+        :type filename: string with filename or JSON-serialized dict (i.e. string) or a dictionary or Geometry instance.
         :return: itself with updated parameters
         """
-        try:
-            if os.path.exists(filename):
-                with open(filename) as f:
-                    dico = json.load(f)
-            else:
-                dico = json.loads(filename)
-        except Exception:
-            logger.info("Unable to parse %s as JSON file, defaulting to PoniParser", filename)
+        poni = None
+        if isinstance(filename, ponifile.PoniFile):
+            poni = filename
+        elif isinstance(filename, (dict, Geometry)):
             poni = ponifile.PoniFile(data=filename)
+        elif isinstance(filename, str):
+            try:
+                if os.path.exists(filename):
+                    with open(filename) as f:
+                        dico = json.load(f)
+                else:
+                    dico = json.loads(filename)
+            except Exception:
+                logger.info("Unable to parse %s as JSON file, defaulting to PoniParser", filename)
+                poni = ponifile.PoniFile(data=filename)
+            else:
+                config = integration_config.ConfigurationReader(dico)
+                poni = config.pop_ponifile()
         else:
-            config = integration_config.ConfigurationReader(dico)
-            poni = config.pop_ponifile()
-        self._init_from_poni(poni)
-
+            logger.error("Unable to initialize geometry from %s", filename)
+        if poni:
+            self._init_from_poni(poni)
         return self
 
     read = load
@@ -1891,6 +1899,9 @@ def polarization(self, shape=None, factor=None, axis_offset=0, with_checksum=Fal
         if isinstance(factor, PolarizationDescription):
             desc = factor
             factor, axis_offset = desc
+        elif isinstance(factor, list) and len(factor)==2:
+            desc = PolarizationDescription(*factor)
+            factor, axis_offset = desc
         else:
             factor = float(factor)
             axis_offset = float(axis_offset)

src/pyFAI/gui/diffmap_widget.py

@@ -31,7 +31,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "27/01/2025"
+__date__ = "03/02/2025"
 __status__ = "development"
 __docformat__ = 'restructuredtext'
 
@@ -155,7 +155,7 @@ class DiffMapWidget(qt.QWidget):
     def __init__(self):
         qt.QWidget.__init__(self)
 
-        self.integration_config = {}
+        self.integration_config = None
         self.list_dataset = ListDataSet()  # Contains all datasets to be treated.
 
         try:
@@ -526,16 +526,15 @@ def process(self, config=None):
         last_processed_file = None
         with self.processing_sem:
             config = self.dump()
-            config_ai = config.get("ai", {})
-            config_ai = config_ai.copy()
+            config_ai = self.integration_config
             diffmap_kwargs = {}
 
-            diffmap_kwargs["nbpt_rad"] = config_ai.get("nbpt_rad")
+            diffmap_kwargs["nbpt_rad"] = config_ai.nbpt_rad
             for key in ["nbpt_fast", "nbpt_slow"]:
                 if key in config:
                     diffmap_kwargs[key] = config[key]
-            if config_ai.get("do_2D"):
-                diffmap_kwargs["nbpt_azim"] = config_ai.get("nbpt_azim", 1)
+            if config_ai.do_2D:
+                diffmap_kwargs["nbpt_azim"] = config_ai.nbpt_azim
 
             diffmap = DiffMap(**diffmap_kwargs)
             diffmap.inputfiles = [i.path for i in self.list_dataset]  # in case generic detector without shape

src/pyFAI/gui/pilx/MainWindow.py

@@ -33,7 +33,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "27/01/2025"
+__date__ = "31/01/2025"
 __status__ = "development"
 
 from typing import Tuple
@@ -62,7 +62,7 @@
 from .widgets.MapPlotWidget import MapPlotWidget
 from .widgets.TitleWidget import TitleWidget
 from ...io.integration_config import WorkerConfig
-
+logger = logging.getLogger(__name__)
 
 class MainWindow(qt.QMainWindow):
     sigFileChanged = qt.Signal(str)
@@ -175,26 +175,24 @@ def initData(self,
             try:
                 image_grp = h5file[path]
             except KeyError:
-                error_msg = f"Cannot access diffraction images at {path}: no such path."
-                logging.warning(error_msg)
-                status_bar = self.statusBar()
-                if status_bar:
-                    status_bar.showMessage(error_msg)
+                self.warning(f"Cannot access diffraction images at {path}: no such path.")
             else:
-                if not isinstance(image_grp, h5py.Group):
-                    error_msg = f"Cannot access diffraction images at {path}: not a group."
-                    logging.warning(error_msg)
-                    status_bar = self.statusBar()
-                    if status_bar:
-                        status_bar.showMessage(error_msg)
-                else:
+                if isinstance(image_grp, h5py.Group):
                     lst = []
                     for key in image_grp:
-                        if key.startswith(base) and isinstance(image_grp[key], h5py.Dataset):
-                            lst.append(key)
+                        try:
+                            ds = image_grp[key]
+                        except KeyError:
+                            self.warning(f"Cannot access diffraction images at {path}/{key}: not a valid dataset.")
+                        else:
+                            if key.startswith(base) and isinstance(ds, h5py.Dataset):
+                                lst.append(key)
+
                     lst.sort()
                     for key in lst:
                         self._dataset_paths[posixpath.join(path, key)] = len(image_grp[key])
+                else:
+                    self.warning(f"Cannot access diffraction images at {path}: not a group.")
 
         self._radial_matrix = compute_radial_values(self.worker_config)
         self._delta_radial_over_2 = delta_radial / 2
@@ -252,20 +250,20 @@ def displayImageAtIndices(self, indices: ImageIndices):
             nxprocess = h5file[self._nxprocess_path]
             map_shape = get_dataset(nxprocess, "result/intensity").shape
             image_index = row * map_shape[1] + col + self._offset
-            for dataset_path, size in self._dataset_paths.items():
-                if image_index < size:
-                    break
-                else:
-                    image_index -= size
+            if self._dataset_paths:
+                for dataset_path, size in self._dataset_paths.items():
+                    if image_index < size:
+                        break
+                    else:
+                        image_index -= size
+            else:
+                self.warning(f"No diffraction data images found in {self._file_name}")
+                return
             try:
                 image_dset = get_dataset(h5file, dataset_path)
             except KeyError:
                 image_link = h5file.get(dataset_path, getlink=True)
-                error_msg = f"Cannot access diffraction images at {image_link}"
-                logging.warning(error_msg)
-                status_bar = self.statusBar()
-                if status_bar:
-                    status_bar.showMessage(error_msg)
+                self.warning(f"Cannot access diffraction images at {image_link}")
                 return
 
             if image_index >= len(image_dset):
@@ -464,3 +462,13 @@ def setNewBackgroundCurve(self, x: float, y: float):
     def clearPoints(self):
         for indices in self._fixed_indices.copy():
             self.removeMapPoint(indices=indices)
+
+    def warning(self, error_msg):
+        """Log a warning both in the terminal and in the status bar if possible
+
+        :param error_msg: string with the message
+        """
+        logger.warning(error_msg)
+        status_bar = self.statusBar()
+        if status_bar:
+            status_bar.showMessage(error_msg)