Merge pull request #104 from michaelmarty/v3

Version 8.0.0 Beta Version

.gitignore

@@ -221,8 +221,8 @@ unidec/bin/Example Data/GroEL UniDec_unidecfiles/GroEL UniDec_report.pdf
 unidec/bin/Example Data/BSA_unidecfiles/BSA_ofile_crazy.dat
 unidec/bin/Example Data/BSA_unidecfiles/BSA_report.html
 unidec_src/UniDec/test_match.bat
-unidec/LipiDec/LipyDec.py
-unidec/LipiDec/SkyQuant.py
+Scripts/LipiDec/LipyDec.py
+Scripts/LipiDec/SkyQuant.py
 docker_commands.txt
 unidec/bin/Example Data/BSA_unidecfiles/BSA_conv.bin
 .pypirc
@@ -272,5 +272,17 @@ unidec/modules/gui_elements/UniDec.mplstyle
 Dockerfile_isodec
 unidec/recent.txt
 unidec/src/UniDec/
-
-
+unidec/IsoDec/src2/
+unidec/IsoDec/test.py
+unidec/IsoDec/testlooper.py
+unidec/IsoDec/oldisodecfunctions.py
+Scripts/MTM/HR/Old/src_vs/
+unidec/IsoDec/src_cmake/cmake-build*
+unidec/IsoDec/src_cmake/.idea/
+unidec/IsoDec/IsoDec tests/
+unidec/IsoDec/bin/
+unidec/IsoDec/lib/
+unidec/IsoDec/src_vs/
+unidec/bin/Example Data/IsoDec/test2_unidecfiles*
+unidec/bin/Example Data/IsoDec/test9_unidecfiles*
+unidec/UniDecImporter/reader_tester.py

Dockerfile

@@ -1,10 +1,10 @@
 FROM python:3.11.9-bookworm
 
 # C dependencies
-RUN apt-get update && apt-get install -y libfftw3-dev hdf5-tools libhdf5-dev --no-install-recommends && rm -rf /var/lib/apt/lists/*
+RUN apt-get update && apt-get install -y libfftw3-dev hdf5-tools libhdf5-dev cmake --no-install-recommends && rm -rf /var/lib/apt/lists/*
 
 # To Run GUI
-RUN pip install setuptools attrdict attrdict3 numpy pymzml networkx natsort h5py matplotlib scipy pyteomics mpld3 pandas plotly
+RUN pip install setuptools attrdict attrdict3 numpy pymzml networkx natsort h5py matplotlib scipy pyteomics mpld3 pandas plotly numba
 # RUN pip install wxpython
 
 # Copy in stuff
@@ -15,6 +15,10 @@ COPY . /opt/UniDec
 WORKDIR /opt/UniDec/unidec/src/
 RUN /opt/UniDec/unidec/src/compilelinux.sh
 
+# Compile IsoDec C
+WORKDIR /opt/UniDec/unidec/IsoDec/src_cmake/
+RUN /opt/UniDec/unidec/IsoDec/src_cmake/compilelinux.sh
+
 # Install Python
 WORKDIR /opt/UniDec/
 RUN python setupdocker.py install
@@ -23,4 +27,5 @@ RUN python setupdocker.py install
 ENV PATH="$PATH:/opt/UniDec/unidec/bin"
 
 # Test everything
-ENV TESTFILE /opt/UniDec/unidec/bin/TestSpectra/test_1.txt
+ENV TESTFILE="/opt/UniDec/unidec/bin/TestSpectra/test_1.txt"
+ENV TESTFILE2="/opt/UniDec/unidec/bin/TestSpectra/test_2.txt"

GUniDec.spec

@@ -74,7 +74,7 @@ hiddenimportslist=['scipy.special._ufuncs_cxx', 'scipy.linalg.cython_blas', 'sci
 
 
 excludeslist = ['IPython', 'statsmodels', 'pyopenms', 'sklearn',
-                       'GdkPixbuf', 'pyQT4', 'pygobject', 'pygtk', 'pyside', 'PySide2', 'shiboken2', 'PyQt5']
+                       'GdkPixbuf', 'pyQT4', 'pygobject', 'pygtk', 'pyside', 'PySide2', 'shiboken2', 'PyQt5', 'torch']
 
 # Analysis of packages
 a = Analysis(['unidec\\Launcher.py'],
@@ -105,15 +105,34 @@ if system == "Windows":
             a.datas += add
             # print add
 
-    a.datas += [('RawFileReaderLicense.doc', 'unidec\\modules\\thermo_reader\\RawFileReaderLicense.doc', 'BINARY')]
-    a.datas += [('ThermoFisher.CommonCore.Data.dll', 'unidec\\modules\\thermo_reader\\ThermoFisher.CommonCore.Data.dll', 'BINARY')]
-    a.datas += [('ThermoFisher.CommonCore.RawFileReader.dll', 'unidec\\modules\\thermo_reader\\ThermoFisher.CommonCore.RawFileReader.dll', 'BINARY')]
-    a.datas += [('ThermoFisher.CommonCore.MassPrecisionEstimator.dll', 'unidec\\modules\\thermo_reader\\ThermoFisher.CommonCore.MassPrecisionEstimator.dll', 'BINARY')]
-    a.datas += [('ThermoFisher.CommonCore.BackgroundSubtraction.dll', 'unidec\\modules\\thermo_reader\\ThermoFisher.CommonCore.BackgroundSubtraction.dll', 'BINARY')]
+    a.datas += [('RawFileReaderLicense.doc', 'unidec\\UniDecImporter\\Thermo\\RawFileReaderLicense.doc', 'BINARY')]
+    a.datas += [('ThermoFisher.CommonCore.Data.dll', 'unidec\\UniDecImporter\\Thermo\\ThermoFisher.CommonCore.Data.dll', 'BINARY')]
+    a.datas += [('ThermoFisher.CommonCore.RawFileReader.dll', 'unidec\\UniDecImporter\\Thermo\\ThermoFisher.CommonCore.RawFileReader.dll', 'BINARY')]
+    a.datas += [('ThermoFisher.CommonCore.MassPrecisionEstimator.dll', 'unidec\\UniDecImporter\\Thermo\\ThermoFisher.CommonCore.MassPrecisionEstimator.dll', 'BINARY')]
+    a.datas += [('ThermoFisher.CommonCore.BackgroundSubtraction.dll', 'unidec\\UniDecImporter\\Thermo\\ThermoFisher.CommonCore.BackgroundSubtraction.dll', 'BINARY')]
     a.datas += [('Waters_MassLynxSDK_EULA.txt', 'unidec\\bin\\Waters_MassLynxSDK_EULA.txt', 'DATA')]
+
+    a.datas += [('BaseCommon.dll', 'unidec\\UniDecImporter\\Agilent\\BaseCommon.dll', 'BINARY')]
+    a.datas += [('BaseCommon.tlb', 'unidec\\UniDecImporter\\Agilent\\BaseCommon.tlb', 'BINARY')]
+    a.datas += [('BaseDataAccess.dll', 'unidec\\UniDecImporter\\Agilent\\BaseDataAccess.dll', 'BINARY')]
+    a.datas += [('BaseDataAccess.tlb', 'unidec\\UniDecImporter\\Agilent\\BaseDataAccess.tlb', 'BINARY')]
+    a.datas += [('BaseError.dll', 'unidec\\UniDecImporter\\Agilent\\BaseError.dll', 'BINARY')]
+    a.datas += [('BaseTof.dll', 'unidec\\UniDecImporter\\Agilent\\BaseTof.dll', 'BINARY')]
+    a.datas += [('MassSpecDataReader.dll', 'unidec\\UniDecImporter\\Agilent\\MassSpecDataReader.dll', 'BINARY')]
+    a.datas += [('MassSpecDataReader.tlb', 'unidec\\UniDecImporter\\Agilent\\MassSpecDataReader.tlb', 'BINARY')]
+
+
+    a.datas += [('isodeclib.dll', 'unidec\\IsoDec\\isodeclib.dll', 'BINARY')]
+    a.datas += [('isodeclib.lib', 'unidec\\IsoDec\\isodeclib.lib', 'BINARY')]
+    a.datas += [('isogenmass.dll', 'unidec\\IsoDec\\isogenmass.dll', 'BINARY')]
+    a.datas += [('isogenmass.lib', 'unidec\\IsoDec\\isogenmass.lib', 'BINARY')]
+
+
 elif system == "Linux":
     a.datas += [('unideclinux', 'unidec/bin/unideclinux', 'BINARY')]
 
+
+
 a.datas += [('cacert.pem', os.path.join('unidec\\bin', 'cacert.pem'), 'DATA')]
 a.datas += [('logo.ico', 'unidec\\bin\\logo.ico', 'DATA')]
 a.datas += [('mass_table.csv', 'unidec\\bin\\mass_table.csv', 'DATA')]
@@ -124,8 +143,6 @@ a.datas += [('UniDecLogoMR.png', 'unidec\\bin\\UniDecLogoMR.png', 'DATA')]
 
 a.datas.extend(dir_files(os.path.join(os.path.dirname(pymzml.__file__), 'obo'), 'obo'))
 
-a.datas.extend(dir_files("unidec\\bin\\multiplierz", 'multiplierz'))
-
 a.datas.extend(dir_files("unidec\\bin\\Presets", 'Presets'))
 a.datas.extend(dir_files("unidec\\bin\\Example Data", 'Example Data'))
 a.datas.extend(dir_files(compat.base_prefix + '\\Lib\\site-packages\\matchms\\data', "matchms\\data"))
@@ -135,9 +152,8 @@ newdir = "numpy/DLLs"
 a.datas.extend(dir_files(mkldir, newdir, type="BINARY"))
 #a.datas.extend(
 #    [(mkldir + "/" + mkl, newdir, 'BINARY') for mkl in listdir(mkldir) if mkl.startswith('mkl_') or mkl.startswith('libio')])
-
-rdkitlibs = compat.base_prefix + "/Lib/site-packages/rdkit.libs"
-a.datas.extend(dir_files(rdkitlibs, ''))
+# rdkitlibs = compat.base_prefix + "/Lib/site-packages/rdkit.libs"
+# a.datas.extend(dir_files(rdkitlibs, ''))
 
 # Assemble and build
 pyz = PYZ(a.pure)

build.bat

@@ -11,5 +11,5 @@ rem update docs with .\unidec_doc\make.bat html
 rem paste docs into UniDecDocumentation and push to git
 
 echo "Building"
-C:\Python311\Scripts\pyinstaller.exe GUniDec.spec --noconfirm
+C:\Python312\Scripts\pyinstaller.exe GUniDec.spec --noconfirm
 rem call "C:\Python\UniDec3\dist\UniDec_Windows\GUI_UniDec.exe"

readme.md

@@ -222,6 +222,26 @@ Of course, using the pre-compiled version means you don't need to know Python at
 
 ## Change Log
 
+v.8.0.0
+
+Added **IsoDec** for isotopic deconvolution. This is a new window that allows you to deconvolve isotopic distributions. It is built using a neural net engine but has a similar interface to conventional UniDec.
+
+New IsoGen neural net for generating isotopic distributions. Used by IsoDec but also available in Python code and via DLL.
+
+Complete rewrite and restructuring of Importing code into UniDecImporter library. This should help harmonize and centralize the MS file reading functions. Removed some prior reliance on multiplierz for Agilent data.
+
+To simplify the import functions, the UniDec GUI has changed slightly such that you need to explicity switch it to ion mobility mode (see Advanced menu) before opening ion mobility files.
+
+Various other under the hood changes to accomodate new code, and some bug fixes.
+
+Fixed label for DAR mode in UPP help files. 
+
+v. 7.0.3
+
+Added check box in UPP to allow all PNG images rather than SVG images, which can improve file sizes.
+
+Added "Config Data Subbuff" to UPP to allow background subtraction with a curved background in the spreadsheet format. Added "Config Data Binevery", "Config Data Lintype", and "Config Data Smoothing" to provide access to other data processing parameters in the spreadsheet format.
+
 v.7.0.2
 
 Improvements to UPP outputs. Fixed issue with reports getting overwritten if the same file is used in multiple rows with UPP. 

setup.py

@@ -16,6 +16,6 @@
     package_data={"": [ "readme.md", "LICENSE"]},
     exclude_package_data={"": ["Scripts", "Scripts.*", "*.Scripts", "*.Scripts.*", ".gitignore", "unidec_doc"],
                           },
-    download_url='https://github.com/michaelmarty/UniDec/archive/refs/tags/v.5.2.1.tar.gz',
+
     classifiers=[],
 )

setupdocker.py

@@ -10,7 +10,7 @@
     url="https://github.com/michaelmarty/UniDec",
     python_requires='>=3.7',
 
-    install_requires=["numpy>=1.16", "scipy>=1.2", "matplotlib>=3.1", "lxml", 'pandas',
+    install_requires=["numpy>=1.16", "scipy>=1.2", "matplotlib>=3.1", "lxml", 'pandas', 'numba',
                       "pymzml", "natsort", "networkx", "h5py", "pyimzml", "pyteomics", "lxml_html_clean"],
 
     packages=find_packages(exclude=["Scripts", "Scripts.*", "*.Scripts", "*.Scripts.*"]),

unidec/DataCollector.py

@@ -12,7 +12,8 @@
 from pubsub import pub
 import platform
 import multiprocessing
-from unidec.modules import UniFit, Extract2D, unidecstructure, PlotAnimations, PlottingWindow, IM_functions
+from unidec.modules import UniFit, Extract2D, unidecstructure, IM_functions
+from unidec.modules.plotting import PlottingWindow, PlotAnimations
 from unidec.modules import DoubleDec, MassDefects, miscwindows
 import unidec.tools as ud
 from unidec.modules.AutocorrWindow import AutocorrWindow
@@ -1490,4 +1491,6 @@ def OnDropFiles(self, x, y, filenames):
     frame = DataCollector(None, "Collect Data")
     app.MainLoop()
 
+    # Test file Z:\mtmarty\Data\Others\cprog\New\Man9 141015\collection2.json
+