Merge pull request #257 from European-XFEL/dev

0.9.1

README.md

@@ -13,9 +13,9 @@ EXtra-foam
 
 ![Overview](docs/images/extra_foam_0.9.0.jpg)
 
-*EXtra-foam* (previously known as *[karaboFAI](https://in.xfel.eu/readthedocs/docs/karabofai/en/latest/)*) is a 
-framework that provides super fast on-line (real-time) and off-line data analysis and visualization for 
-experiments at European XFEL that using 2D detectors (e.g. AGIPD, DSSC, LPD, ePix100, FastCCD, JungFrau, 
-etc.), together with other 1D detectors (e.g. XGM, digitizer, etc.) and various control data.
+*EXtra-foam* is a framework that provides real-time and off-line data analysis (**detector geometry**, 
+**pump-probe**, **azimuthal integration**, **ROI**, **statistics**, etc.) and visualization for experiments 
+that use **2D area detectors** (*AGIPD*, *LPD*, *DSSC*, *FastCCD*, *JungFrau*, *ePix100*, etc.) and 
+**1D detectors** (*Gotthard*, *XGM*, *digitizer*, etc.) at European XFEL.
 
 [Documentation](https://extra-foam.readthedocs.io/en/latest/)

benchmarks/azimuthal_integration.ipynb

@@ -0,0 +1,171 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# EXtra-foam azimuthal integration benchmark"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os.path as osp\n",
+    "\n",
+    "import numpy as np\n",
+    "from pyFAI.azimuthalIntegrator import AzimuthalIntegrator as PyfaiAzimuthalIntegrator\n",
+    "from scipy.signal import find_peaks\n",
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "import extra_foam\n",
+    "print(extra_foam.__version__)\n",
+    "\n",
+    "from extra_foam.algorithms import AzimuthalIntegrator, ConcentricRingsFinder\n",
+    "from extra_foam.algorithms import mask_image_data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def load_image(filepath):\n",
+    "    img = np.load(osp.join(osp.expanduser('~'), filepath))\n",
+    "    mask = np.zeros_like(img, dtype=bool)\n",
+    "    mask_image_data(img, out=mask)\n",
+    "    _, ax = plt.subplots(figsize=(12, 12))\n",
+    "    ax.imshow(img)\n",
+    "    \n",
+    "    return img, mask\n",
+    "\n",
+    "# img, mask = load_image(\"jf_ring.npy\")\n",
+    "img, mask = load_image(\"jf_ring_6modules.npy\")\n",
+    "# img, mask = load_image(\"lpd.npy\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dist = 1  # sample distance\n",
+    "npt = 1024  # number of integration points\n",
+    "pixel1, pixel2 = 0.75e-6, 0.75e-6  # pixel size (y, x)\n",
+    "cy, cx = 537, 1132 \n",
+    "poni1, poni2 = cy * pixel1, cx * pixel2  # integration center (y, x)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# %%timeit\n",
+    "\n",
+    "pyfai_integrator = PyfaiAzimuthalIntegrator(\n",
+    "    dist=dist, poni1=poni1, poni2=poni2, pixel1=pixel1, pixel2=pixel2, wavelength=1e-10)\n",
+    "\n",
+    "q_gt, I_gt = pyfai_integrator.integrate1d(img, npt, mask=mask, unit=\"q_A^-1\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# %%timeit\n",
+    "\n",
+    "integrator = AzimuthalIntegrator(\n",
+    "    dist=dist, poni1=poni1, poni2=poni2, pixel1=pixel1, pixel2=pixel2, wavelength=1e-10)\n",
+    "\n",
+    "q, I = integrator.integrate1d(img, npt=npt)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "_, ax = plt.subplots(figsize=(12, 6))\n",
+    "\n",
+    "ax.plot(1e-10 * q, I, '-', label='EXtra-foam')\n",
+    "ax.plot(q_gt, I_gt, '--', label='pyFAI')\n",
+    "ax.set_xlabel(\"q (1/A)\", fontsize=16)\n",
+    "ax.set_ylabel(\"I (arb.)\", fontsize=16)\n",
+    "ax.legend(fontsize=16)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# %%timeit\n",
+    "\n",
+    "min_count = 500\n",
+    "prominence = 100\n",
+    "distance = 10\n",
+    "\n",
+    "finder = ConcentricRingsFinder(pixel2, pixel1)\n",
+    "cx, cy = finder.search(img, cx, cy, min_count=min_count)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "q, s = finder.integrate(img, cx, cy, min_count=min_count)\n",
+    "\n",
+    "i_peaks = find_peaks(s, distance=distance, prominence=prominence)[0]\n",
+    "\n",
+    "_, ax = plt.subplots(figsize=(12, 6))\n",
+    "\n",
+    "ax.plot(q, s, '-')\n",
+    "ax.plot(q[i_peaks], s[i_peaks], 'x')\n",
+    "ax.set_xlabel(\"Radial (pixel)\", fontsize=16)\n",
+    "ax.set_ylabel(\"I (arb.)\", fontsize=16)\n",
+    "\n",
+    "print(\"Optimized cx = \", cx, \", cy = \", cy)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "foam-gcc6",
+   "language": "python",
+   "name": "foam-gcc6"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

benchmarks/gui/benchmark_imageview.py

@@ -8,6 +8,7 @@
 All rights reserved.
 """
 import time
+from collections import deque
 
 import numpy as np
 
@@ -21,6 +22,8 @@
 
 class BenchmarkImageViewSpeed:
     def __init__(self):
+        self._dt = deque(maxlen=60)
+
         self._timer = QTimer()
         self._timer.timeout.connect(self.update)
 
@@ -40,9 +43,9 @@ def update(self):
         self._count += 1
 
         now = time.time()
-        dt = now - self._prev_t
+        self._dt.append(now - self._prev_t)
         self._prev_t = now
-        fps = 1.0/dt
+        fps = len(self._dt) / sum(self._dt)
 
         self._view.setTitle(f"{fps:.2f} fps")
 

benchmarks/gui/benchmark_plotwidget.py

@@ -9,6 +9,7 @@
 """
 import time
 from enum import IntEnum
+from collections import deque
 
 import numpy as np
 
@@ -29,24 +30,28 @@ class PlotType(IntEnum):
 
 class BenchmarkPlotItemSpeed:
     def __init__(self, plot_type=PlotType.Line):
+        self._dt = deque(maxlen=60)
+
         self._timer = QTimer()
         self._timer.timeout.connect(self.update)
+        # self._timer.singleShot(1, self.update)
 
         self._widget = PlotWidgetF()
+        self._widget.addLegend()
 
         if plot_type == PlotType.Line:
-            self._graph = self._widget.plotCurve()
+            self._graph = self._widget.plotCurve(name='line')
             n_pts = 5000
         elif plot_type == PlotType.Bar:
-            self._graph = self._widget.plotBar()
+            self._graph = self._widget.plotBar(name='bar')
             n_pts = 300
         elif plot_type == PlotType.StatisticsBar:
-            self._graph = self._widget.plotStatisticsBar()
+            self._graph = self._widget.plotStatisticsBar(name='statistics bar')
             self._graph.setBeam(1)
             n_pts = 500
         elif plot_type == PlotType.Scatter:
-            self._graph = self._widget.plotScatter()
-            n_pts = 3000
+            self._graph = self._widget.plotScatter(name='scatter')
+            n_pts = 5000
         else:
             raise ValueError(f"Unknown plot type: {plot_type}")
 
@@ -77,16 +82,16 @@ def update(self):
         self._count += 1
 
         now = time.time()
-        dt = now - self._prev_t
+        self._dt.append(now - self._prev_t)
         self._prev_t = now
-        fps = 1.0 / dt
+        fps = len(self._dt) / sum(self._dt)
 
         self._widget.setTitle(f"{fps:.2f} fps")
 
         app.processEvents()  # force complete redraw for every plot
 
 
 if __name__ == '__main__':
-    bench = BenchmarkPlotItemSpeed(PlotType.Line)
+    bench = BenchmarkPlotItemSpeed(PlotType.Scatter)
     bench.start()
     app.exec_()

docs/changelog.rst

@@ -1,6 +1,26 @@
 CHANGELOG
 =========
 
+0.9.1 (15 July 2020)
+------------------------
+
+- **Bug Fix**
+
+  - Fix transform type update in TransformView in ImageTool. #251
+
+- **Improvement**
+
+  - PlotItem will not be shown in legend if its name is empty. #254
+  - Improve y2-axis plot implementation. #253
+  - Improve stack detector modules. #247
+  - Implement ScatterPlotItem to replace the pyqtgraph one. #238
+
+- **New Feature**
+
+  - Implement curve fitting in correlation window. #255
+  - Implement azimuthal integration and concentric ring detection in C++. #252
+
+
 0.9.0 (30 June 2020)
 ------------------------