Merge pull request #198 from European-XFEL/dev

0.8.3 Release

.travis.yml

@@ -95,11 +95,10 @@ script:
   # test parallel version
   - python setup.py build_ext --with-tests
   - python setup.py test -v
+  - python setup.py benchmark -v
 
   # test series version
-  - export FOAM_WITH_TBB=0
-  - export FOAM_WITH_XSIMD=0
-  - export XTENSOR_WITH_TBB=0
-  - export XTENSOR_WITH_XSIMD=0
+  - export BUILD_SERIAL_FOAM=1
   - python setup.py build_ext --with-tests
   - python setup.py test -v
+  - python setup.py benchmark -v

benchmarks/benchmark_statistics.py

@@ -8,34 +8,54 @@
 )
 
 
-def benchmark_nan(f_cpp, f_py, shape):
-    data = np.random.randn(*shape)
-    data[::2, ::2] = np.nan
+def benchmark_nan_without_axis(f_cpp, f_py, shape, dtype):
+    data = np.random.randn(*shape).astype(dtype) + 1.  # shift to avoid very small mean
+    data[:, :3, ::3] = np.nan
 
     t0 = time.perf_counter()
-    for i in range(100):
-        ret_cpp = f_cpp(data)
+    ret_cpp = f_cpp(data)
     dt_cpp = time.perf_counter() - t0
 
     t0 = time.perf_counter()
-    for i in range(100):
-        ret_py = f_py(data)
+    ret_py = f_py(data)
     dt_py = time.perf_counter() - t0
 
-    assert ret_cpp == pytest.approx(ret_py)
+    assert ret_cpp == pytest.approx(ret_py, rel=1e-4)
 
-    print(f"\n{f_cpp.__name__} with {float} - \n"
+    print(f"\nwithout axis, dtype = {dtype} - \n"
+          f"dt (cpp): {dt_cpp:.4f}, "
+          f"dt (numpy): {dt_py:.4f}")
+
+
+def benchmark_nan_keep_zero_axis(f_cpp, f_py, shape, dtype):
+    data = np.random.randn(*shape).astype(dtype=dtype) + 1.  # shift to avoid very small mean
+    data[:, :3, ::3] = np.nan
+
+    t0 = time.perf_counter()
+    ret_cpp = f_cpp(data, axis=(-2, -1))
+    dt_cpp = time.perf_counter() - t0
+
+    t0 = time.perf_counter()
+    ret_py = f_py(data, axis=(-2, -1))
+    dt_py = time.perf_counter() - t0
+
+    assert ret_cpp == pytest.approx(ret_py, rel=1e-4)
+
+    print(f"\nkeep zero axis, dtype = {dtype} - \n"
           f"dt (cpp): {dt_cpp:.4f}, "
           f"dt (numpy): {dt_py:.4f}")
 
 
 if __name__ == "__main__":
     print("*" * 80)
-    print("Benchmark image processing")
+    print("Benchmark statistics functions")
     print("*" * 80)
 
-    s = (1096, 1120)
+    s = (16, 1096, 1120)
 
-    for f_cpp, f_py in [(nanmean, np.nanmean),
-                        (nansum, np.nansum)]:
-        benchmark_nan(f_cpp, f_py, s)
+    for f_cpp, f_py in [(nansum, np.nansum), (nanmean, np.nanmean)]:
+        print(f"\n----- {f_cpp.__name__} ------")
+        benchmark_nan_without_axis(f_cpp, f_py, s, np.float32)
+        benchmark_nan_without_axis(f_cpp, f_py, s, np.float64)
+        benchmark_nan_keep_zero_axis(f_cpp, f_py, s, np.float32)
+        benchmark_nan_keep_zero_axis(f_cpp, f_py, s, np.float64)

docs/changelog.rst

@@ -1,6 +1,47 @@
 CHANGELOG
 =========
 
+0.8.3 (11 May 2020)
+------------------------
+
+- **Breaking change**
+    - In the terminal, "--n_modules 2" is required to run JungFrauPR with two modules. #41
+
+- **Bug Fix**
+    - Change pixel size of ePix100 from 0.11 mm to 0.05 mm. #189
+
+- **Improvement**
+    - Mask tile/ASIC edges by default. #192
+    - Improve geometry 1M and its unittest. #190
+    - Invert y axis for displayed image. #187
+    - Rename geometry to geometry_1m in C++. #186
+    - Improve tr-XAS analysis in special suite. #163 #183
+    - Improve correlating error message. #182
+    - Improve documentation for special suite. #177
+    - New reset interface in special suite. #170
+    - Regularize names of methods and attributes in special suite. #167
+    - Add new mode, start/end train ID control and progress bar, etc. in FileStreamer. #166
+    - Move definition of meta source from config to SourceCatalog. #165
+    - Use correlated queue in special suite. #164
+    - Improve shape comparing error message in C++. #160
+    - Improve mask image data implementation and interface. #157
+    - Move image assembler into image processor. # 155
+    - Refactor masking code. #149
+    - Implement generic binding for nansum and nanmean. #114
+
+- **New Feature**
+    - Add axis calibration in Gotthard analysis. #179
+    - Implement generalized geometry for multi-module detectors. #175 #196
+    - Implement streaming JungFrauPR data from files. #174
+    - Implement Gotthard pump-probe analysis in special suite. #173 #178
+    - Add ROI histogram in CameraView in special suite. #172
+    - Add ROI control in special suite. #171
+    - Implement XAS-TIM-XMCD in special suite. #162
+    - Implement MultiCameraView in special suite. #147
+    - Implement XAS-TIM in special suite. #146
+    - Implement load and save mask in pixel coordinates. #132 #154 #185 #191 #197
+
+
 0.8.2 (8 April 2020)
 ------------------------
 

docs/config_file.rst

@@ -29,29 +29,29 @@ The first block of the config file looks like the following:
                     FXE_DET_LPD1M-1/DET/*CH0:xtdf:
                         - image.data
 
-        JungFrau:
-            PIPELINE:
-                FXE_XAD_JF1M/DET/RECEIVER-1:display:
-                    - data.adc
-                FXE_XAD_JF1M/DET/RECEIVER-2:display:
-                    - data.adc
-
-        XGM:
-            CONTROL:
-                SA1_XTD2_XGM/DOOCS/MAIN:
-                    - pulseEnergy.photonFlux
-                    - beamPosition.ixPos
-                    - beamPosition.iyPos
-            PIPELINE:
-                SA1_XTD2_XGM/DOOCS/MAIN:output:
-                    - data.intensitySa1TD
-
-        Motor:
-            CONTROL:
-                FXE_SMS_USR/MOTOR/UM01:
-                    - actualPosition
-                FXE_SMS_USR/MOTOR/UM02:
-                    - actualPosition
+            JungFrau:
+                PIPELINE:
+                    FXE_XAD_JF1M/DET/RECEIVER-1:display:
+                        - data.adc
+                    FXE_XAD_JF1M/DET/RECEIVER-2:display:
+                        - data.adc
+
+            XGM:
+                CONTROL:
+                    SA1_XTD2_XGM/DOOCS/MAIN:
+                        - pulseEnergy.photonFlux
+                        - beamPosition.ixPos
+                        - beamPosition.iyPos
+                PIPELINE:
+                    SA1_XTD2_XGM/DOOCS/MAIN:output:
+                        - data.intensitySa1TD
+
+            Motor:
+                CONTROL:
+                    FXE_SMS_USR/MOTOR/UM01:
+                        - actualPosition
+                    FXE_SMS_USR/MOTOR/UM02:
+                        - actualPosition
 
 
 The next block of the config file looks like the following:

docs/developer.rst

@@ -58,8 +58,12 @@ Release **EXtra-foam**
 - Update the version number in `extra_foam/__init__.py`;
 - Merge the above change into the `dev` branch;
 - Merge the `dev` branch into the `master` branch;
-- Tag the `master` branch.
-
+- Tag the `master` branch;
+- Create a new branch from the new `master` branch and update the version number in
+  `extra_foam/__init__.py`. For example, if the latest release version is "0.8.0",
+  the new version number should be "0.8.1dev", supposing the next release is 0.8.1.
+  Also, the name of the new branch should be "0.8.1dev";
+- Merge the new branch into the `dev` branch;
 
 Deployment on EuXFEL Anaconda Environment
 """""""""""""""""""""""""""""""""""""""""