Merge pull request #245 from European-XFEL/dev

0.9.0
European-XFEL · Jun 30, 2020 · 03117a2 · 03117a2
2 parents f8f2502 + 679427e
commit 03117a2
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diff --git a/.travis.yml b/.travis.yml
@@ -23,13 +23,13 @@ jobs:
       env: PYTHON_VERSION="3.7.5" COMPILER="gcc" GCCv="7"
     - stage: full linux
       os: linux
-      env: PYTHON_VERSION="3.7.5" COMPILER="gcc" GCCv="7"
+      env: PYTHON_VERSION="3.7.5" COMPILER="gcc" GCCv="8"
     - stage: full linux
       os: linux
-      env: PYTHON_VERSION="3.7.5" COMPILER="gcc" GCCv="6"
+      env: PYTHON_VERSION="3.7.5" COMPILER="gcc" GCCv="7"
     - stage: full linux
       os: linux
-      env: PYTHON_VERSION="3.6.9" COMPILER="gcc" GCCv="7"
+      env: PYTHON_VERSION="3.7.5" COMPILER="gcc" GCCv="6"
     - stage: full linux
       os: linux
       env: PYTHON_VERSION="3.6.9" COMPILER="gcc" GCCv="6"
@@ -86,7 +86,7 @@ before_install:
 install:
   - conda install -y python=$PYTHON_VERSION
   - echo $PYTHON_VERSION
-  - conda install -y cmake libstdcxx-ng numpy -c anaconda
+  - conda install -y cmake numpy -c anaconda
   - conda install -y -c conda-forge tbb-devel
   - export CMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"}
   - pip install -e .[test]

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -59,6 +59,8 @@ if(FOAM_USE_TBB OR XTENSOR_USE_TBB)
     set(TBB_REQUIRED_VERSION 2020.1)
     string(REPLACE "." "_U" TBB_REQUIRED_VERSION_STR ${TBB_REQUIRED_VERSION})
 
+    add_compile_definitions(TBB_SUPPRESS_DEPRECATED_MESSAGES)
+
     find_package(TBB QUIET)
     if(TBB_FOUND AND ${TBB_VERSION_MAJOR}.${TBB_VERSION_MINOR} VERSION_EQUAL TBB_REQUIRED_VERSION)
         set(TBB_LIBRARY ${TBB_LIBRARIES_RELEASE})
@@ -146,6 +148,17 @@ if(BUILD_FOAM_TESTS)
     add_subdirectory(test)
 endif()
 
+# ============
+# Build flags
+# ============
+
+if(CMAKE_CXX_COMPILER_VERSION)
+    set(FOAM_COMPILER_STR "${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER_ARG1} (version ${CMAKE_CXX_COMPILER_VERSION})")
+else()
+    set(FOAM_COMPILER_STR "${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER_ARG1}")
+endif()
+string(STRIP "${FOAM_COMPILER_STR}" FOAM_COMPILER_STR)
+
 # ============
 # Installation
 # ============

diff --git a/README.md b/README.md
@@ -11,6 +11,8 @@ EXtra-foam
 ![Language](https://img.shields.io/badge/language-c++-red)
 [![Qt 5](https://img.shields.io/badge/Qt-5-brightgreen)](https://doc.qt.io/qt-5/)
 
+![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, 

diff --git a/benchmarks/gui/benchmark_imageview.py b/benchmarks/gui/benchmark_imageview.py
@@ -0,0 +1,55 @@
+"""
+Distributed under the terms of the BSD 3-Clause License.
+
+The full license is in the file LICENSE, distributed with this software.
+
+Author: Jun Zhu <[email protected]>
+Copyright (C) European X-Ray Free-Electron Laser Facility GmbH.
+All rights reserved.
+"""
+import time
+
+import numpy as np
+
+from PyQt5.QtCore import QTimer
+
+from extra_foam.gui import mkQApp
+from extra_foam.gui.plot_widgets import ImageViewF
+
+app = mkQApp()
+
+
+class BenchmarkImageViewSpeed:
+    def __init__(self):
+        self._timer = QTimer()
+        self._timer.timeout.connect(self.update)
+
+        self._data = np.random.normal(size=(50, 1024, 1280))
+        self._prev_t = None
+        self._count = 0
+
+        self._view = ImageViewF()
+        self._view.show()
+
+    def start(self):
+        self._prev_t = time.time()
+        self._timer.start(0)
+
+    def update(self):
+        self._view.setImage(self._data[self._count % 10])
+        self._count += 1
+
+        now = time.time()
+        dt = now - self._prev_t
+        self._prev_t = now
+        fps = 1.0/dt
+
+        self._view.setTitle(f"{fps:.2f} fps")
+
+        app.processEvents()  # force complete redraw for every plot
+
+
+if __name__ == '__main__':
+    bench = BenchmarkImageViewSpeed()
+    bench.start()
+    app.exec_()
diff --git a/benchmarks/gui/benchmark_plotwidget.py b/benchmarks/gui/benchmark_plotwidget.py
@@ -0,0 +1,92 @@
+"""
+Distributed under the terms of the BSD 3-Clause License.
+
+The full license is in the file LICENSE, distributed with this software.
+
+Author: Jun Zhu <[email protected]>
+Copyright (C) European X-Ray Free-Electron Laser Facility GmbH.
+All rights reserved.
+"""
+import time
+from enum import IntEnum
+
+import numpy as np
+
+from PyQt5.QtCore import QTimer
+
+from extra_foam.gui import mkQApp
+from extra_foam.gui.plot_widgets import PlotWidgetF
+
+app = mkQApp()
+
+
+class PlotType(IntEnum):
+    Line = 0
+    Bar = 1
+    StatisticsBar = 2
+    Scatter = 3
+
+
+class BenchmarkPlotItemSpeed:
+    def __init__(self, plot_type=PlotType.Line):
+        self._timer = QTimer()
+        self._timer.timeout.connect(self.update)
+
+        self._widget = PlotWidgetF()
+
+        if plot_type == PlotType.Line:
+            self._graph = self._widget.plotCurve()
+            n_pts = 5000
+        elif plot_type == PlotType.Bar:
+            self._graph = self._widget.plotBar()
+            n_pts = 300
+        elif plot_type == PlotType.StatisticsBar:
+            self._graph = self._widget.plotStatisticsBar()
+            self._graph.setBeam(1)
+            n_pts = 500
+        elif plot_type == PlotType.Scatter:
+            self._graph = self._widget.plotScatter()
+            n_pts = 3000
+        else:
+            raise ValueError(f"Unknown plot type: {plot_type}")
+
+        self._x = np.arange(n_pts)
+        self._data = 100 * np.random.normal(size=(50, n_pts))
+        if plot_type == PlotType.StatisticsBar:
+            self._y_min = self._data - 20
+            self._y_max = self._data + 20
+        self._plot_type = plot_type
+
+        self._prev_t = None
+        self._count = 0
+
+        self._widget.show()
+
+    def start(self):
+        self._prev_t = time.time()
+        self._timer.start(0)
+
+    def update(self):
+        idx = self._count % 10
+        if self._plot_type == PlotType.StatisticsBar:
+            self._graph.setData(self._x, self._data[idx],
+                                y_min=self._y_min[idx], y_max=self._y_max[idx])
+        else:
+            self._graph.setData(self._x, self._data[idx])
+
+        self._count += 1
+
+        now = time.time()
+        dt = now - self._prev_t
+        self._prev_t = now
+        fps = 1.0 / dt
+
+        self._widget.setTitle(f"{fps:.2f} fps")
+
+        app.processEvents()  # force complete redraw for every plot
+
+
+if __name__ == '__main__':
+    bench = BenchmarkPlotItemSpeed(PlotType.Line)
+    bench.start()
+    app.exec_()
diff --git a/docs/changelog.rst b/docs/changelog.rst
@@ -1,6 +1,39 @@
 CHANGELOG
 =========
 
+0.9.0 (30 June 2020)
+------------------------
+
+- **Bug Fix**
+
+  - Fix bug in data source tree introduced in 0.8.4. #235
+  - Fix transparent Nan pixel with the latest pyqtgraph version. #231
+
+- **Improvement**
+
+  - Improve performance of PlotCurveItem and add benchmarks for PlotItems and ImageViewF. #243
+  - Make ctrl widgets in Imagetool more compact. #241
+  - Improve C++ code quality and suppress TBB deprecate warning. #239
+  - Add meter bar to plot area. #236
+  - Reimplement ImageItem and PlotItem to replace the pyqtgraph ones. #232 #242
+  - Improve data source updating and color encoding matched source items in
+    the data source tree. #230 #234
+  - Rename configurator to analysis setup manager and allow take snapshot for
+    each setup. #228
+  - Update data source and trouble shooting in documentation. #227
+  - Add summary of compiler flags for EXtra-foam-python. #226
+  - Update installation (gcc7) and CI (gcc8). #226
+  - Rename misleading mouse mode in the right-click context menu. #211
+  - Update pyqtgraph to the latest master branch. #206 #211 #233
+
+- **New Feature**
+
+  - Annotate peaks in azimuthal integration view. #240
+  - Enable Legend for all the plot items. #206 #237
+  - Implement logarithmic X/Y scale in right-click context menu. #206
+  - Enable C++ API installation and add examples. #227
+
+
 0.8.4 (8 June 2020)
 ------------------------
 

diff --git a/docs/config_file.rst b/docs/config_file.rst
@@ -6,14 +6,18 @@ CONFIG FILE
 Users from different instruments should use the corresponding config file to config
 the instrument specific data sources, the detector specific setups and so on.
 
+Each instrument has a default config file, which can be found in the
+`github repository <https://github.com/European-XFEL/EXtra-foam/tree/dev/extra_foam/configs>`__.
+We appreciate if the beamline scientists can help us keep the default config file updated.
+
 Let's take *FXE* for example, when one starts a detector on topic *FXE* for the first by
 time:
 
 .. code-block:: bash
 
     extra-foam LPD FXE
 
-, the system will create a new config file `$HOME/.EXtra-foam/fxe.config.yaml`.
+, the system will create a new config file `$HOME/.EXtra-foam/fxe.config.yaml` using the default one.
 The first block of the config file looks like the following:
 
 .. code-block:: yaml

diff --git a/docs/image_tool.rst b/docs/image_tool.rst
@@ -1,3 +1,5 @@
+.. _Image tool:
+
 IMAGE TOOL
 ==========
 
@@ -247,8 +249,8 @@ aforementioned coordinate system, respectively.
 .. image:: images/pyFAI_PONI.png
    :width: 800
 
-.. image:: images/azimuthal_integ_1D.png
-   :width: 800
+.. image:: images/azimuthal_integ_1D.jpg
+
 
 +----------------------------+--------------------------------------------------------------------+
 | Input                      | Description                                                        |
@@ -288,6 +290,27 @@ aforementioned coordinate system, respectively.
 |                            | azimuthal integration result.                                      |
 +----------------------------+--------------------------------------------------------------------+
 
+By default, peak finding is activated and peak positions will be annotated along the scattering
+curve if the number of detected peaks is between 1 and 10. There is no special reason for choosing
+10 as the upper limit. Nevertheless, if there are two many peaks found, it may be due to a noisy
+scattering curve or some unreasonable peak-finding parameters.
+
+For now, users can set prominence to refine the number of detected peaks and use a slicer to select
+part of them. The prominence of a peak measures how much a peak stands out from the surrounding
+baseline of the signal and is defined as the vertical distance between the peak and its lowest
+contour line. The slicer is useful when the scattering curve has some undesired structure, especially
+at the start and/or end of the curve.
+
++----------------------------+--------------------------------------------------------------------+
+| Input                      | Description                                                        |
++============================+====================================================================+
+| ``Peak finding``           | Check to activate real-time peak finding and annotating.           |
++----------------------------+--------------------------------------------------------------------+
+| ``Peak prominence``        | Minimum prominence of peaks.                                       |
++----------------------------+--------------------------------------------------------------------+
+| ``Peak slicer``            | Pixel size along the detector's 2nd dimension.                     |
++----------------------------+--------------------------------------------------------------------+
+
 
 .. _Geometry:
 

diff --git a/docs/images/1d_binning.jpg b/docs/images/1d_binning.jpg
diff --git a/docs/images/analysis_setup_manager.png b/docs/images/analysis_setup_manager.png
diff --git a/docs/images/analysis_setup_manager_context_menu.png b/docs/images/analysis_setup_manager_context_menu.png
diff --git a/docs/images/azimuthal_integ_1D.jpg b/docs/images/azimuthal_integ_1D.jpg
diff --git a/docs/images/azimuthal_integ_1D.png b/docs/images/azimuthal_integ_1D.png
diff --git a/docs/images/binning_setup.png b/docs/images/binning_setup.png
diff --git a/docs/images/binning_window.png b/docs/images/binning_window.png
diff --git a/docs/images/configurator.png b/docs/images/configurator.png
diff --git a/docs/images/correlation.jpg b/docs/images/correlation.jpg
diff --git a/docs/images/correlation_setup.png b/docs/images/correlation_setup.png
diff --git a/docs/images/correlation_window.png b/docs/images/correlation_window.png
diff --git a/docs/images/data_source_tree.png b/docs/images/data_source_tree.png
diff --git a/docs/images/extra_foam_0.9.0.jpg b/docs/images/extra_foam_0.9.0.jpg
diff --git a/docs/images/main_gui_action_bar.jpg b/docs/images/main_gui_action_bar.jpg
diff --git a/docs/images/source_monitor.png b/docs/images/source_monitor.png
diff --git a/docs/images/special_suite_camera_view.jpg b/docs/images/special_suite_camera_view.jpg
diff --git a/docs/images/special_suite_gotthard.jpg b/docs/images/special_suite_gotthard.jpg
diff --git a/docs/images/special_suite_gotthard_pump_probe.jpg b/docs/images/special_suite_gotthard_pump_probe.jpg
diff --git a/docs/index.rst b/docs/index.rst
@@ -11,6 +11,7 @@ Contents:
    introduction
    installation
    start
+   trouble_shooting
    config_file
    main_gui
    image_tool

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -19,9 +19,18 @@ In your Anaconda_ environment, run the following commands:
 
 .. code-block:: bash
 
-    $ conda install -c anaconda cmake libstdcxx-ng numpy
+    # install gcc-6.1
     $ conda install -c omgarcia gcc-6
-    $ conda install -c conda-forge tbb
+    $ conda install -c anaconda libstdcxx-ng
+
+    # install gcc-7.5 (experimenting)
+    # $ conda install -c conda-forge gxx_linux-64
+    # $ ln -s ${CONDA_PREFIX}/bin/x86_64-conda_cos6-linux-gnu-gcc  ${CONDA_PREFIX}/bin/gcc
+    # $ ln -s ${CONDA_PREFIX}/bin/x86_64-conda_cos6-linux-gnu-g++  ${CONDA_PREFIX}/bin/g++
+
+    # install cmake and dependencies
+    $ conda install -c anaconda cmake numpy
+    $ conda install -c conda-forge tbb-devel
 
 Install **EXtra-foam**
 ----------------------
@@ -55,7 +64,5 @@ Install C++ API of **EXtra-foam** only
 .. code-block:: bash
 
     $ mkdir build && cd build
-    $ cmake -DFOAM_USE_TBB=ON -DXTENSOR_USE_TBB=ON
-            -DFOAM_USE_XSIMD=ON -DXTENSOR_USE_XSIMD=ON -march=native
-            -DCMAKE_INSTALL_PREFIX=/YOUR/INSTALL/PREFIX
+    $ cmake -DFOAM_USE_XSIMD=ON -DCMAKE_INSTALL_PREFIX=/YOUR/INSTALL/PREFIX
     $ make && make install
diff --git a/docs/introduction.rst b/docs/introduction.rst
@@ -1,6 +1,9 @@
 INTRODUCTION
 ============
 
+.. image:: images/extra_foam_0.9.0.jpg
+
+
 **EXtra-foam** ( **F**\ ast **O**\ nline **A**\ nalysis **M**\ onitor) is a tool that provides
 real-time and off-line data analysis (**azimuthal integration**, **ROI**, **correlation**,
 **binning**, etc.) and visualization for experiments using **2D area detectors** (*AGIPD*,
@@ -75,34 +78,3 @@ can be preprocessed and analysed per second.
     Due to the limited performance of `PyQt`, the visualization rate could be slower
     than the processing rate if there are too many plots to render, especially for
     train-resolved detectors.
-
-
-Galleries
----------
-
-.. image:: images/MainGUI.png
-   :width: 800
-
-.. image:: images/ImageTool.png
-   :width: 800
-
-.. image:: images/pump_probe_window.png
-   :width: 800
-
-.. image:: images/correlation_window.png
-   :width: 800
-
-.. image:: images/histogram_window.png
-   :width: 800
-
-.. image:: images/binning_window.png
-   :width: 800
-
-.. image:: images/special_suite_tr_xas.png
-   :width: 800
-
-.. image:: images/special_suite_xas_tim.png
-   :width: 800
-
-.. image:: images/special_suite_xas_tim_xmcd.png
-   :width: 800