[pyFAI-integrate] FiberIntegrator batch

doc/source/changelog.rst

@@ -41,6 +41,10 @@ Change-log of versions
   * Documentation with a new tutorial on carbon polymorphs (diamond, graphite and C60)
 - [integrate1|2d] enforce arguments to be kwargs to limit user errors
 - [Doc] Improve the notebook about "flatfield" calculation.
+- [Fiber/GrazingIncidence]
+  * Compatibility with pyFAI-integrate GUI and Worker
+  * Build the missing wedge mask using percentile threshold of counts
+
 - [Integrate1/2dResult] 
 
   * can perform some basic maths (+, -), uncertainties are propagated accordingly.

src/pyFAI/app/integrate.py

@@ -47,10 +47,10 @@
 import fabio
 from .. import utils, io, version as pyFAI_version, date as pyFAI_date
 from ..io import DefaultAiWriter, HDF5Writer
-from ..io.integration_config import WorkerConfig
+from ..io.integration_config import WorkerConfig, WorkerFiberConfig
 from ..utils.shell import ProgressBar
 from ..utils import logging_utils, header_utils
-from ..worker import Worker
+from ..worker import Worker, WorkerFiber
 logging.basicConfig(level=logging.INFO)
 logging.captureWarnings(True)
 logger = logging.getLogger(__name__)
@@ -82,7 +82,13 @@ def moveCenterTo(window, center):
 
     def validateConfig():
         config = window.get_config()
-        reason = Worker.validate_config(config, raise_exception=None)
+        integrator_class = config.get("integrator_class", "AzimuthalIntegrator")
+        if integrator_class == "AzimuthalIntegrator":
+            reason = Worker.validate_config(config, raise_exception=None)
+        elif integrator_class == "FiberIntegrator":
+            reason = WorkerFiber.validate_config(config, raise_exception=None)
+        else:
+            raise TypeError(f"{integrator_class} is not a valid integrator class")
         if reason is None:
             processData(config)
         else:
@@ -121,8 +127,13 @@ def processData(config=None):
         if config is None:
             config = window.get_worker_config()
         elif isinstance(config, dict):
-            config = WorkerConfig.from_dict(config)
-
+            integrator_class = config.get("integrator_class", "AzimuthalIntegrator")
+            if integrator_class == "AzimuthalIntegrator":
+                config = WorkerConfig.from_dict(config)
+            elif integrator_class == "FiberIntegrator":
+                config = WorkerFiberConfig.from_dict(config)
+            else:
+                raise TypeError(f"{integrator_class} is not a valid integrator class")
         dialog = IntegrationProcess(None)
         dialog.adjustSize()
         moveCenterTo(dialog, center)
@@ -627,11 +638,24 @@ def process(input_data, output, config, observer, write_mode=HDF5Writer.MODE_ERR
         # Create a null observer to avoid to deal with None
         observer = IntegrationObserver()
 
-    worker = Worker()
-    if isinstance(config, WorkerConfig):
+    if isinstance(config, dict):
+        integrator_class = config.get("integrator_class", "AzimuthalIntegrator")
+        if integrator_class == "AzimuthalIntegrator":
+            worker_config = WorkerConfig.from_dict(config)
+            worker = Worker()
+        elif integrator_class == "FiberIntegrator":
+            worker_config = WorkerFiberConfig.from_dict(config)
+            worker = WorkerFiber()
+        else:
+            raise TypeError(f"{integrator_class} is not a valid integrator class")
+    elif type(config) is WorkerConfig:
+        worker_config = config
+        worker = Worker()
+    elif type(config) is WorkerFiberConfig:
         worker_config = config
+        worker = WorkerFiber()
     else:
-        worker_config = WorkerConfig.from_dict(config)
+        raise TypeError(f"{config} should be dictionary, WorkerConfig or WorkerFiberConfig")
 
     monitor_name = worker_config.monitor_name
     worker.set_config(worker_config)

src/pyFAI/gui/IntegrationDialog.py

@@ -116,13 +116,19 @@ def __displayResultUpdated(self):
 
     def __displayResult(self, result, resetZoom=False):
         self._plot.clear()
-        if isinstance(result, containers.Integrate1dResult):
-            self._plot.setGraphXLabel("Radial")
+        if isinstance(result, (containers.Integrate1dResult, containers.Integrate1dFiberResult)):
+            if isinstance(result, containers.Integrate1dFiberResult):
+                self._plot.setGraphXLabel("Integrated (in-plane / out-of-plane)")
+                edges = result.integrated
+            else:
+                self._plot.setGraphXLabel("Radial")
+                edges = result.radial
             self._plot.setGraphYLabel("Intensity")
+
             self._plot.addHistogram(
                 legend="result1d",
                 align="center",
-                edges=result.radial,
+                edges=edges,
                 color="blue",
                 histogram=result.intensity,
                 resetzoom=False)
@@ -152,6 +158,33 @@ def computeLocation(result):
                 scale=scale,
                 colormap=DEFAULT_COLORMAP,
                 resetzoom=False)
+        elif isinstance(result, containers.Integrate2dFiberResult):
+
+            def computeLocation(result):
+                # Assume that axes are linear
+                if result.intensity.shape[1] > 1:
+                    scaleX = (result.inplane[-1] - result.inplane[0]) / (result.intensity.shape[1] - 1)
+                else:
+                    scaleX = 1.0
+                if result.intensity.shape[0] > 1:
+                    scaleY = (result.outofplane[-1] - result.outofplane[0]) / (result.intensity.shape[0] - 1)
+                else:
+                    scaleY = 1.0
+                halfPixel = 0.5 * scaleX, 0.5 * scaleY
+                origin = (result.inplane[0] - halfPixel[0], result.outofplane[0] - halfPixel[1])
+                return origin, (scaleX, scaleY)
+
+            self._plot.setGraphXLabel("In-plane")
+            self._plot.setGraphYLabel("Out-of-plane")
+            origin, scale = computeLocation(result)
+            self._plot.addImage(
+                legend="result2d",
+                data=result.intensity,
+                origin=origin,
+                scale=scale,
+                colormap=DEFAULT_COLORMAP,
+                resetzoom=False)
+
         else:
             logger.error("Unsupported result type %s", type(result))
         if resetZoom:

src/pyFAI/gui/widgets/WorkerConfigurator.py

@@ -46,7 +46,7 @@
 from ..dialog.GeometryDialog import GeometryDialog
 from ..dialog.IntegrationMethodDialog import IntegrationMethodDialog
 from ...utils import float_, str_, get_ui_file
-from ...units import RADIAL_UNITS, to_unit, Unit, UnitFiber, parse_fiber_unit
+from ...units import RADIAL_UNITS, to_unit, Unit, UnitFiber
 from ..model.GeometryModel import GeometryModel
 from ..model.DataModel import DataModel
 from ..utils import units
@@ -607,7 +607,7 @@ def normalizeFiles(filenames):
             self.do_oop_range.setChecked(wc.do_oop_range)
             self.vertical_integration.setChecked(wc.vertical_integration)
             self.do_1d_integration.setChecked(wc.integration_1d)
-            unit_ip = parse_fiber_unit(**wc.unit_ip)
+            unit_ip = wc.unit_ip
 
             # In UnitSelector, searching the unit is made with 'is' not '==', not valid for FiberUnit (which are copies)
             for index in range(self.ip_unit.count()):
@@ -616,7 +616,7 @@ def normalizeFiles(filenames):
                     self.ip_unit.setCurrentIndex(index)
                     break
 
-            unit_oop = parse_fiber_unit(**wc.unit_oop)
+            unit_oop = wc.unit_oop
             for index in range(self.oop_unit.count()):
                 item = self.oop_unit.itemData(index)
                 if item == unit_oop: