Merge pull request #2524 from kif/2512_pilx_zigzag

Implement the storage of the `map_ptr` in

Author: kif

src/pyFAI/diffmap.py

@@ -30,7 +30,7 @@
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "28/04/2025"
+__date__ = "14/05/2025"
 __status__ = "development"
 __docformat__ = 'restructuredtext'
 
@@ -56,8 +56,7 @@
 from .io.ponifile import PoniFile
 from .worker import Worker
 from .utils.decorators import deprecated, deprecated_warning
-
-DIGITS = [str(i) for i in range(10)]
+from string import digits as DIGITS
 Position = collections.namedtuple('Position', 'index slow fast')
 
 
@@ -105,6 +104,7 @@ def __init__(self, nbpt_fast=0, nbpt_slow=1, nbpt_rad=1000, nbpt_azim=None,
         self.nxdata_grp = None
         self.dataset = None
         self.dataset_error = None
+        self.map_ptr = None
         self.inputfiles = []
         self.timing = []
         self.stats = False
@@ -524,6 +524,11 @@ def makeHDF5(self, rewrite=False):
         fast_motor_ds.attrs["interpretation"] = "scalar"
         fast_motor_ds.attrs["long_name"] = self.fast_motor_name
 
+        self.map_ptr = self.nxdata_grp.create_dataset("map_ptr", shape=(self.nbpt_slow,self.nbpt_fast), dtype=numpy.int32)
+        self.map_ptr.attrs["interpretation"] = "image"
+        self.map_ptr.attrs["long_name"] = "Frame index for given map position"
+
+
         if self.worker.do_2D():
             self.dataset = self.nxdata_grp.create_dataset(
                             name="intensity",
@@ -719,24 +724,33 @@ def set_hdf5_input_dataset(self, dataset):
             return
         else:
             self.stored_input.add(id_)
-        # Process 0: measurement group
+        # Process 0: measurement group & source group
         if "measurement" in self.entry_grp:
             measurement_grp = self.entry_grp["measurement"]
         else:
             measurement_grp = self.nxs.new_class(self.entry_grp, "measurement", "NXdata")
+
+        if "source" in self.nxdata_grp.parent:
+            source_grp = self.nxdata_grp.parent["source"]
+        else:
+            source_grp = self.nxs.new_class(self.nxdata_grp.parent, "source", "NXcollection")
+
         here = os.path.dirname(os.path.abspath(self.nxs.filename))
         there = os.path.abspath(dataset.file.filename)
         name = f"images_{len(self.stored_input):04d}"
-        measurement_grp[name] = h5py.ExternalLink(os.path.relpath(there, here), dataset.name)
+        source_grp[name] = measurement_grp[name] = h5py.ExternalLink(os.path.relpath(there, here), dataset.name)
+
         if "signal" not in measurement_grp.attrs:
             measurement_grp.attrs["signal"] = name
 
+
     def process_one_frame(self, frame):
         """
         :param frame: 2d numpy array with an image to process
         """
         self._idx += 1
         pos = self.get_pos(None, self._idx)
+        self.map_ptr[pos.slow, pos.fast] = self._idx
         shape = self.dataset.shape
         if pos.slow + 1 > shape[0]:
             self.dataset.resize((pos.slow + 1,) + shape[1:])

src/pyFAI/gui/diffmap_widget.py

@@ -30,7 +30,7 @@
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "13/05/2025"
+__date__ = "14/05/2025"
 __status__ = "development"
 __docformat__ = 'restructuredtext'
 
@@ -704,7 +704,7 @@ def update_slice(self, *args):
         """
         Update the slice
         """
-        logger.info("update_slice", args)
+        logger.info("DiffMapWidget.update_slice %s", args)
         if self.radial_data is None:
             return
         try:

src/pyFAI/gui/matplotlib.py

@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (C) 2016-2018 European Synchrotron Radiation Facility
+# Copyright (C) 2016-2025 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -33,7 +33,7 @@
 
 __authors__ = ["T. Vincent"]
 __license__ = "MIT"
-__date__ = "13/05/2025"
+__date__ = "16/05/2025"
 
 import sys
 import logging
@@ -54,22 +54,18 @@ def _configure(backend, backend_qt4=None, check=False):
             valid = valid and matplotlib.rcParams['backend.qt4'] == backend_qt4
 
         if not valid:
-            _logger.warning('matplotlib already loaded, setting its backend may not work')
+            msg = f'Matplotlib already loaded with backend `{matplotlib.rcParams["backend"]}`, setting its backend to `{backend}` may not work!'
+            _logger.warning(msg)
         return
     matplotlib.rcParams['backend'] = backend
     if backend_qt4 is not None:
         matplotlib.rcParams['backend.qt4'] = backend_qt4
 
-
 if qt.BINDING in ('PySide', 'PyQt4'):
     _configure('Qt4Agg', qt.BINDING, check=_check_matplotlib)
     from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg  # noqa
 
-elif qt.BINDING in ('PyQt5', 'PySide2'):
-    _configure('Qt5Agg', check=_check_matplotlib)
-    from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg  # noqa
-
-elif qt.BINDING in ('PyQt6', 'PySide6'):
+elif qt.BINDING in ('PyQt6', 'PySide6', 'PyQt5', 'PySide2'):
     _configure('QtAgg', check=_check_matplotlib)
     from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg  # noqa
 

src/pyFAI/gui/pilx/MainWindow.py

@@ -33,10 +33,11 @@
 __contact__ = "loic.huder@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "20/02/2025"
+__date__ = "16/05/2025"
 __status__ = "development"
 
 from typing import Tuple
+from string import digits
 import json
 import h5py
 import logging
@@ -117,6 +118,9 @@ def __init__(self) -> None:
         self._background_point = None
         self.worker_config = None
 
+        # declaration of instance variables
+        self._map_ptr = None # This is the map of the indices of input frame
+
     def initData(self,
                  file_name: str,
                  dataset_path: str="/entry_0000/measurement/images_0001",
@@ -134,14 +138,14 @@ def initData(self,
             map_data = get_dataset(nxprocess, "result/intensity")[()].sum(axis=-1)
             try:
                 slow = get_dataset(nxprocess, "result/slow")
-            except Exception:
+            except (KeyError, RuntimeError):
                 slow_label = slow_values = None
             else:
                 slow_label = slow.attrs.get("long_name", "Y")
                 slow_values = slow[()]
             try:
                 fast = get_dataset(nxprocess, "result/fast")
-            except Exception:
+            except (KeyError, RuntimeError):
                 fast_values = fast_label = None
             else:
                 fast_label = fast.attrs.get("long_name", "X")
@@ -164,15 +168,14 @@ def initData(self,
             else:
                 self._offset = 0
 
-            # Find source dataset paths
-            cnt = 0
-            for char in dataset_path[-1::-1]:
-                if char.isdigit():
-                    cnt += 1
-                else:
-                    break
+            try:
+                self._map_ptr = get_dataset(nxprocess, "result/map_ptr")[()]
+            except (KeyError, RuntimeError):
+                logger.warning("No `map_ptr` dataset in NXdata: guessing the frame indices !")
+                self._map_ptr = numpy.arange(self._offset, self._offset + map_data.size)
+                self._map_ptr.shape = map_data.shape
 
-            _dataset_path = dataset_path[:-cnt]
+            _dataset_path = dataset_path.rstrip(digits)
             path, base = posixpath.split(_dataset_path)
 
             try:
@@ -282,7 +285,12 @@ def displayImageAtIndices(self, indices: ImageIndices):
         with h5py.File(self._file_name, "r") as h5file:
             nxprocess = h5file[self._nxprocess_path]
             map_shape = get_dataset(nxprocess, "result/intensity").shape
-            image_index = row * map_shape[1] + col + self._offset
+            if self._map_ptr is None:
+                logger.warning("No `map_ptr` defined: guessing the frame indices !")
+                image_index = row * map_shape[1] + col + self._offset
+            else:
+                image_index = self._map_ptr[row, col]
+
             if self._dataset_paths:
                 for dataset_path, size in self._dataset_paths.items():
                     if image_index < size:

src/pyFAI/io/diffmap_config.py

@@ -31,16 +31,19 @@
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "28/04/2025"
+__date__ = "14/05/2025"
 __status__ = "development"
 __docformat__ = 'restructuredtext'
 
 import os
+import posixpath
 import copy
 import json
 import logging
 logger = logging.getLogger(__name__)
 from collections import namedtuple
+import numpy
+import h5py
 from .tree import TreeItem
 from .integration_config import dataclass, ClassVar, WorkerConfig, fields, asdict
 from .nexus import is_hdf5
@@ -55,7 +58,7 @@ class MotorRange:
 
     :param start: Begining of the movement
     :param stop: End of the movement, included
-    :param step: Number of points (i.e. numberof steps + 1)
+    :param points: Number of points (i.e. numberof steps + 1)
     :param name: Name of the motor
     """
     start: float = None
@@ -83,9 +86,13 @@ def __repr__(self):
 
     @property
     def step_size(self):
-        if self.points < 1:
+        if self.points < 2:
             return
-        return (self.stop-self.start)/self.points
+        return (self.stop-self.start)/self.steps
+
+    @property
+    def steps(self):
+        return self.points-1
 
     @classmethod
     def _parse_old_config(cls, dico, prefix="slow"):
@@ -104,6 +111,74 @@ def _parse_old_config(cls, dico, prefix="slow"):
             self.stop = float(rng[-1])
         return self
 
+
+def parse_bliss(filename, motors, transpose=False):
+    """Parse a bliss master file (HDF5) for 2 motors which were scanned
+    and calculate the frame index of each pixel, returned as a map.
+
+    :param filename: name of the Bliss master file
+    :param motors: 2-tuple of 1d-datasets names in the masterfile. Both have the same shape.
+    :param transpose: set to True to have the fast dimention along y instead of x.
+    :return: map_ptr, [MotorRange_y, MotorRange_x]
+    """
+    def build_dict(posi):
+        "histogram like procedure with dict"
+        dico = {}
+        for i in posi:
+            if i in dico:
+                dico[i]+=1
+            else:
+                dico[i]=0
+        return dico
+
+    if len(motors) != 2:
+        raise RuntimeError("Expected a list of 2 path pointing to 1d datasets, got {motors}!")
+
+    #read all motor position datasets
+    motor_raw = {}
+    with h5py.File(filename) as h:
+        for name in motors:
+            motor_raw[name] = h[name][()]
+
+    if (motor_raw[motors[0]].shape != motor_raw[motors[1]].shape):
+        raise RuntimeError("Expected a list of 2 1d datasets, with the same shape!")
+
+    ranges = {}
+    for name in motor_raw:
+        dico = build_dict(motor_raw[name])
+        mr = MotorRange(name=posixpath.basename(name))
+        mr.start = min(dico.keys())
+        mr.stop = max(dico.keys())
+        mr.points = len(dico.keys())
+        ranges[name] = mr
+
+    # The slow motor is often still, so its speed is null, much more often than the fast motor.
+    ordered_names = []
+    dm1 = numpy.diff(motor_raw[motors[0]])
+    dm2 = numpy.diff(motor_raw[motors[1]])
+    if (dm1==0).sum()>(dm2==0).sum():
+        ordered_names = motors
+    else:
+        ordered_names = motors[-1::-1]
+    ordered_ranges = [ranges[i] for i in ordered_names]
+
+    slow = ordered_ranges[0]
+    fast = ordered_ranges[1]
+    slow_pos = motor_raw[ordered_names[0]]
+    fast_pos = motor_raw[ordered_names[1]]
+
+    #Build the map
+    map_ptr = numpy.zeros((slow.points, fast.points), dtype=numpy.int32)
+    slow_idx = numpy.round((slow_pos - slow.start) / slow.step_size).astype(int)
+    fast_idx = numpy.round((fast_pos - fast.start) / fast.step_size).astype(int)
+    map_ptr[slow_idx, fast_idx] = numpy.arange(slow.points*fast.points, dtype=int)
+
+    if transpose:
+        return map_ptr.T, ordered_ranges[-1::-1]
+    else:
+        return map_ptr, ordered_ranges
+
+
 DataSetNT = namedtuple("DataSet", ("path", "h5", "nframes", "shape"), defaults=[None, None, None])
 
 @dataclass
@@ -302,7 +377,6 @@ def from_dict(cls, dico, inplace=False):
                     if value is None:
                         to_init[key] = value
                     elif isinstance(value, (list, tuple)):
-                        print(klass, value)
                         if "from_serialized" in dir(klass):
                             to_init[key] = klass.from_serialized(value)
                         else:
@@ -324,8 +398,6 @@ def from_dict(cls, dico, inplace=False):
             self.fast_motor = fast
             self.fast_motor = slow
 
-        # print(self)
-
         for key in cls.GUESSED:
             if key in dico:
                 dico.pop(key)

src/pyFAI/test/test_bug_regression.py

@@ -36,7 +36,7 @@
 __contact__ = "Jerome.Kieffer@esrf.fr"
 __license__ = "MIT"
 __copyright__ = "2015-2024 European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "16/05/2025"
+__date__ = "26/05/2025"
 
 import sys
 import os
@@ -662,9 +662,6 @@ def test_bug_2525(self):
         self.assertEqual(sp.shape, sp_dp.shape)
 
 
-
-
-
 class TestBug1703(unittest.TestCase):
     """
     Check the normalization affect propely the propagated errors/intensity