Merge pull request #21 from zengjiexia/Improve_SR_length_calculation

Update v2.2

ACT_python3.yml

@@ -3,84 +3,176 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - astropy=4.0.2=py36h779f372_0
-  - certifi=2021.5.30=py36ha15d459_0
-  - cycler=0.10.0=py_2
-  - dill=0.3.4=pyhd8ed1ab_0
-  - freetype=2.10.4=h546665d_1
-  - imglyb=2.0.0=pyh8a188c0_0
-  - intel-openmp=2021.3.0=h57928b3_3372
-  - jbig=2.1=h8d14728_2003
-  - jgo=1.0.3=pyhd8ed1ab_0
-  - jpeg=9d=h8ffe710_0
-  - jpype1=1.3.0=py36he95197e_0
-  - kiwisolver=1.3.1=py36he95197e_1
-  - lerc=2.2.1=h0e60522_0
-  - libblas=3.9.0=11_win64_mkl
-  - libcblas=3.9.0=11_win64_mkl
-  - libdeflate=1.7=h8ffe710_5
-  - liblapack=3.9.0=11_win64_mkl
-  - libpng=1.6.37=h1d00b33_2
-  - libtiff=4.3.0=h0c97f57_1
-  - libzlib=1.2.11=h8ffe710_1013
-  - lz4-c=1.9.3=h8ffe710_1
+  - aom=3.5.0=h63175ca_0
+  - astropy=5.2.2=py38h634f036_0
+  - blosc=1.21.4=hdccc3a2_0
+  - brotli=1.0.9=hcfcfb64_8
+  - brotli-bin=1.0.9=hcfcfb64_8
+  - bzip2=1.0.8=h8ffe710_4
+  - c-blosc2=2.9.2=h183a6f4_0
+  - ca-certificates=2023.5.7=h56e8100_0
+  - cairo=1.16.0=hdecc03f_1016
+  - certifi=2023.5.7=pyhd8ed1ab_0
+  - cfitsio=4.2.0=h9ebe7e4_0
+  - charls=2.4.2=h1537add_0
+  - charset-normalizer=3.1.0=pyhd8ed1ab_0
+  - click=8.1.3=win_pyhd8ed1ab_2
+  - cloudpickle=2.2.1=pyhd8ed1ab_0
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - contourpy=1.0.7=py38hb1fd069_0
+  - cycler=0.11.0=pyhd8ed1ab_0
+  - cytoolz=0.12.0=py38h91455d4_1
+  - dask-core=2023.5.0=pyhd8ed1ab_0
+  - dav1d=1.2.1=hcfcfb64_0
+  - dill=0.3.6=pyhd8ed1ab_1
+  - double-conversion=3.2.0=h63175ca_1
+  - et_xmlfile=1.1.0=pyhd8ed1ab_0
+  - expat=2.5.0=h63175ca_1
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=hab24e00_0
+  - fontconfig=2.14.2=hbde0cde_0
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - fonttools=4.40.0=py38h91455d4_0
+  - freetype=2.12.1=h546665d_1
+  - fsspec=2023.6.0=pyh1a96a4e_0
+  - gettext=0.21.1=h5728263_0
+  - giflib=5.2.1=h64bf75a_3
+  - graphite2=1.3.13=1000
+  - harfbuzz=7.3.0=h196d34a_0
+  - icu=72.1=h63175ca_0
+  - idna=3.4=pyhd8ed1ab_0
+  - imagecodecs=2023.1.23=py38h29c013e_2
+  - imageio=2.31.1=pyh24c5eb1_0
+  - imglyb=2.1.0=pyha21a80b_0
+  - importlib-metadata=6.6.0=pyha770c72_0
+  - importlib-resources=5.12.0=pyhd8ed1ab_0
+  - importlib_metadata=6.6.0=hd8ed1ab_0
+  - importlib_resources=5.12.0=pyhd8ed1ab_0
+  - intel-openmp=2023.1.0=h57928b3_46319
+  - jgo=1.0.5=pyhd8ed1ab_0
+  - joblib=1.2.0=pyhd8ed1ab_0
+  - jpype1=1.4.1=py38hb1fd069_1
+  - jxrlib=1.1=h8ffe710_2
+  - kiwisolver=1.4.4=py38hb1fd069_1
+  - krb5=1.20.1=heb0366b_0
+  - labeling=0.1.12=pyhd8ed1ab_1
+  - lcms2=2.15=h3e3b177_1
+  - lerc=4.0.0=h63175ca_0
+  - libaec=1.0.6=h63175ca_1
+  - libavif=0.11.1=ha7b97ba_2
+  - libblas=3.9.0=17_win64_mkl
+  - libbrotlicommon=1.0.9=hcfcfb64_8
+  - libbrotlidec=1.0.9=hcfcfb64_8
+  - libbrotlienc=1.0.9=hcfcfb64_8
+  - libcblas=3.9.0=17_win64_mkl
+  - libclang=16.0.5=default_heb8d277_0
+  - libclang13=16.0.5=default_hc80b9e7_0
+  - libcurl=8.1.2=h68f0423_0
+  - libdeflate=1.18=hcfcfb64_0
+  - libexpat=2.5.0=h63175ca_1
+  - libffi=3.4.2=h8ffe710_5
+  - libglib=2.76.3=he8f3873_0
+  - libhwloc=2.9.1=nocuda_h15da153_6
+  - libiconv=1.17=h8ffe710_0
+  - libjpeg-turbo=2.1.5.1=hcfcfb64_0
+  - liblapack=3.9.0=17_win64_mkl
+  - libpng=1.6.39=h19919ed_0
+  - libsqlite=3.42.0=hcfcfb64_0
+  - libssh2=1.11.0=h7dfc565_0
+  - libtiff=4.5.0=h6c8260b_6
+  - libwebp-base=1.3.0=hcfcfb64_0
+  - libxcb=1.15=hcd874cb_0
+  - libxml2=2.11.4=hc3477c8_0
+  - libxslt=1.1.37=h6070c61_1
+  - libzlib=1.2.13=hcfcfb64_5
+  - libzopfli=1.0.3=h0e60522_0
+  - llvmlite=0.40.0=py38h19421c1_0
+  - locket=1.0.0=pyhd8ed1ab_0
+  - lz4-c=1.9.4=hcfcfb64_0
   - m2w64-gcc-libgfortran=5.3.0=6
   - m2w64-gcc-libs=5.3.0=7
   - m2w64-gcc-libs-core=5.3.0=7
   - m2w64-gmp=6.1.0=2
   - m2w64-libwinpthread-git=5.0.0.4634.697f757=2
-  - matplotlib-base=3.3.4=py36h1abdf75_0
+  - matplotlib-base=3.7.1=py38h528a6c7_0
   - maven=3.6.3=h57928b3_0
-  - mkl=2021.3.0=hb70f87d_564
+  - mkl=2022.1.0=h6a75c08_874
   - msys2-conda-epoch=20160418=1
-  - multiprocess=0.70.12.2=py36h68aa20f_0
-  - numpy=1.19.5=py36h4b40d73_2
-  - olefile=0.46=pyh9f0ad1d_1
-  - openjdk=8.0.302=h57928b3_0
-  - pathos=0.2.7=pyhd3deb0d_0
-  - pillow=8.0.1=py36ha0524ae_0
-  - pip=21.0.1=py36haa95532_0
-  - pox=0.3.0=pyhd8ed1ab_0
-  - ppft=1.6.6.4=pyhd8ed1ab_0
-  - psutil=5.8.0=py36h68aa20f_1
-  - pyimagej=1.0.2=py36ha15d459_0
-  - pyparsing=2.4.7=pyh9f0ad1d_0
-  - python=3.6.13=h3758d61_0
+  - multiprocess=0.70.14=py38h91455d4_3
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - networkx=3.1=pyhd8ed1ab_0
+  - numba=0.57.0=py38hb182ae8_1
+  - numpy=1.24.3=py38h1d91fd2_0
+  - openjdk=8.0.332=h57928b3_0
+  - openjpeg=2.5.0=ha2aaf27_2
+  - openpyxl=3.1.2=py38h91455d4_0
+  - openssl=3.1.1=hcfcfb64_1
+  - packaging=23.1=pyhd8ed1ab_0
+  - pandas=1.5.3=py38h5846ac1_1
+  - partd=1.4.0=pyhd8ed1ab_0
+  - pathos=0.3.0=pyhd8ed1ab_0
+  - pcre2=10.40=h17e33f8_0
+  - pillow=9.5.0=py38ha7eb54a_1
+  - pip=23.1.2=pyhd8ed1ab_0
+  - pixman=0.40.0=h8ffe710_0
+  - platformdirs=3.5.3=pyhd8ed1ab_0
+  - pooch=1.7.0=pyha770c72_3
+  - pox=0.3.2=pyhd8ed1ab_0
+  - ppft=1.7.6.6=pyhd8ed1ab_0
+  - psutil=5.9.5=py38h91455d4_0
+  - pthread-stubs=0.4=hcd874cb_1001
+  - pthreads-win32=2.9.1=hfa6e2cd_3
+  - pyerfa=2.0.0.3=py38hbaf524b_0
+  - pyimagej=1.0.2=py38haa244fe_1
+  - pyparsing=3.0.9=pyhd8ed1ab_0
+  - pyqtgraph=0.13.3=pyhd8ed1ab_0
+  - pyside6=6.5.1=py38hac9af9c_0
+  - pysocks=1.7.1=pyh0701188_6
+  - python=3.8.16=h4de0772_1_cpython
   - python-dateutil=2.8.2=pyhd8ed1ab_0
-  - python_abi=3.6=2_cp36m
-  - pytz=2021.3=pyhd8ed1ab_0
-  - scipy=1.5.2=py36h7ff6e69_2
-  - scyjava=1.3.1=pyhd8ed1ab_0
-  - setuptools=58.0.4=py36haa95532_0
+  - python_abi=3.8=3_cp38
+  - pytz=2023.3=pyhd8ed1ab_0
+  - pywavelets=1.4.1=py38hbaf524b_0
+  - pyyaml=6.0=py38h91455d4_5
+  - qt6-main=6.5.1=hf0c6fff_1
+  - requests=2.31.0=pyhd8ed1ab_0
+  - scikit-image=0.19.3=py38h5846ac1_2
+  - scikit-learn=1.2.2=py38h763eb3e_2
+  - scipy=1.10.1=py38h1aea9ed_3
+  - scyjava=1.9.0=pyhd8ed1ab_0
+  - setuptools=67.7.2=pyhd8ed1ab_0
   - six=1.16.0=pyh6c4a22f_0
-  - sqlite=3.36.0=h2bbff1b_0
-  - tbb=2021.3.0=h2d74725_0
-  - tk=8.6.11=h8ffe710_1
-  - tornado=6.1=py36h68aa20f_1
-  - typing_extensions=3.10.0.2=pyha770c72_0
-  - vc=14.2=h21ff451_1
-  - vs2015_runtime=14.27.29016=h5e58377_2
-  - wheel=0.37.0=pyhd3eb1b0_1
-  - wincertstore=0.2=py36h7fe50ca_0
-  - xarray=0.18.2=pyhd8ed1ab_0
-  - xz=5.2.5=h62dcd97_1
-  - zlib=1.2.11=h8ffe710_1013
-  - zstd=1.5.0=h6255e5f_0
+  - skan=0.11.0=pyhd8ed1ab_0
+  - snappy=1.1.10=hfb803bf_0
+  - tbb=2021.9.0=h91493d7_0
+  - threadpoolctl=3.1.0=pyh8a188c0_0
+  - tifffile=2023.4.12=pyhd8ed1ab_0
+  - tk=8.6.12=h8ffe710_0
+  - toolz=0.12.0=pyhd8ed1ab_0
+  - tqdm=4.65.0=pyhd8ed1ab_1
+  - typing-extensions=4.6.3=hd8ed1ab_0
+  - typing_extensions=4.6.3=pyha770c72_0
+  - ucrt=10.0.22621.0=h57928b3_0
+  - unicodedata2=15.0.0=py38h91455d4_0
+  - urllib3=2.0.3=pyhd8ed1ab_0
+  - vc=14.3=hb25d44b_16
+  - vc14_runtime=14.34.31931=h5081d32_16
+  - vs2015_runtime=14.34.31931=hed1258a_16
+  - wheel=0.40.0=pyhd8ed1ab_0
+  - win_inet_pton=1.1.0=pyhd8ed1ab_6
+  - xarray=2023.1.0=pyhd8ed1ab_0
+  - xorg-libxau=1.0.11=hcd874cb_0
+  - xorg-libxdmcp=1.1.3=hcd874cb_0
+  - xz=5.2.6=h8d14728_0
+  - yaml=0.2.5=h8ffe710_2
+  - zfp=1.0.0=h63175ca_3
+  - zipp=3.15.0=pyhd8ed1ab_0
+  - zlib=1.2.13=hcfcfb64_5
+  - zlib-ng=2.0.7=hcfcfb64_0
+  - zstd=1.5.2=h12be248_6
   - pip:
-    - decorator==4.4.2
-    - imagecodecs==2020.5.30
-    - imageio==2.9.0
-    - joblib==1.1.0
-    - networkx==2.5.1
-    - opencv-contrib-python==4.1.2.30
-    - pandas==0.25.3
-    - pyside6==6.0.2
-    - pywavelets==1.1.1
-    - scikit-image==0.17.2
-    - scikit-learn==0.24.2
-    - shiboken6==6.0.2
-    - sklearn==0.0
-    - threadpoolctl==3.1.0
-    - tifffile==2019.7.26.2
-    - tqdm==4.60.0
+      - opencv-contrib-python==4.7.0.72
 prefix: D:\Anaconda3\envs\ACT_python3

README.md

@@ -37,28 +37,28 @@ Requirements
 
 Full list please see ACT_python3.yml.
 
-- Python 3 (tested with Python 3.6-3.9)
-	- os
-	- sys
-	- re
-	- datatime
-	- [opencv - 4.1.2.30](https://pypi.org/project/opencv-contrib-python/)
-	- [tqdm - 4.60.0](https://pypi.org/project/tqdm/)
-	- [astropy - 4.0.2](https://www.astropy.org/)
-	- [PIL - 8.0.1](https://pypi.org/project/Pillow/)
-	- [scipy - 1.5.2](https://www.scipy.org/)
-	- [numpy](https://numpy.org/)
-	- [math](https://docs.python.org/3/library/math.html)
-	- [tifffile](https://pypi.org/project/tifffile/)
-	- [pandas - 1.4.1](https://pandas.pydata.org/)
-	- [scikit-image - 0.17.2](https://scikit-image.org/)
-	- [scikit-learn - 0.24.2](https://scikit-learn.org/)
-	- [PySide 6 - 6.0.2](https://pypi.org/project/PySide6/)
-	- [pyqtgraph](https://github.com/pyqtgraph/pyqtgraph)(Included locally)
-	- [pathos](https://pypi.org/project/pathos/)
-	- [psutil](https://pypi.org/project/psutil/)
-    - [pyimagej](https://github.com/imagej/pyimagej) (install with conda-forge)
-    - Openjdk - 8
+- Python 3 (configured with Python 3.8.16)
+	- [astropy - 5.2.2](https://www.astropy.org/)
+	- [imageio - 2.31.1](https://anaconda.org/conda-forge/imageio)
+	- [imglyb - 2.1.0](https://anaconda.org/conda-forge/imglyb)
+	- [maven - 3.6.3](https://anaconda.org/conda-forge/maven)
+	- [numpy - 1.24.3](https://numpy.org/)
+	- [opencv-contrib-python - 4.7.0.72](https://pypi.org/project/opencv-contrib-python/)
+    - [openjdk - 8.0.332](https://anaconda.org/conda-forge/openjdk)
+    - [pandas - 1.4.1](https://pandas.pydata.org/)
+	- [pathos](https://anaconda.org/conda-forge/pathos)
+	- [pillow - 9.5.0](https://anaconda.org/conda-forge/pillow)
+	- [psutil](https://anaconda.org/conda-forge/psutil)
+    - [pyimagej - 1.0.2](https://github.com/imagej/pyimagej) (must install with conda-forge)
+	- [pyqtgraph - 0.13.3](https://github.com/pyqtgraph/pyqtgraph)
+    - [PySide 6 - 6.5.1](https://anaconda.org/conda-forge/pyside6)
+	- [scikit-image - 0.19.3](https://scikit-image.org/)
+	- [scikit-learn - 1.2.2](https://scikit-learn.org/)
+	- [scipy - 1.10.1](https://www.scipy.org/)
+    - [scyjava - 1.9.0](https://anaconda.org/conda-forge/scyjava)
+    - [skan - 0.11.0](https://github.com/jni/skan)
+	- [tifffile - 2023.4.12](https://anaconda.org/conda-forge/tifffile)
+	- [tqdm - 4.65.0](https://anaconda.org/conda-forge/tqdm)
 
 - [Fiji(is just imagej)](https://imagej.net/Fiji) 
 	- [ComDet](https://github.com/ekatrukha/ComDet)

UI_form/ACT.pyproject.user

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE QtCreatorProject>
-<!-- Written by QtCreator 4.14.1, 2022-07-26T17:37:17. -->
+<!-- Written by QtCreator 4.14.1, 2023-07-16T08:34:35. -->
 <qtcreator>
  <data>
   <variable>EnvironmentId</variable>