Merge pull request #226 from MannLabs/develop

Develop

Author: sander-willems-bruker

alphatims/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "alphatims"
-__version__ = "1.0.3"
+__version__ = "1.0.4"
 __license__ = "Apache"
 __description__ = "A Python package to index Bruker TimsTOF raw data for fast and easy accession and visualization"
 __author__ = "Sander Willems, Eugenia Voytik"

alphatims/bruker.py

@@ -2271,44 +2271,50 @@ def use_calibrated_mz_values_as_default(
                 )
         self._use_calibrated_mz_values_as_default = use_calibrated_mz_values
 
-
     def set_cycle(self) -> None:
         """Set the quad cycle for diaPASEF data.
         """
-        subframes = self.fragment_frames.drop("Frame", axis=1)
-        for max_index in range(1, len(subframes)):
-            subframe = subframes.iloc[max_index]
-            if subframe.equals(subframes.iloc[0]):
-                break
-        frames = self.fragment_frames.Frame[max_index] - 1
-        frames += (1 - int(self.zeroth_frame))
-        sub_cycles = frames - len(np.unique(self.fragment_frames.Frame[:max_index]))
+        ms1_diffs = np.diff(
+            np.flatnonzero(self.frames.MsMsType[int(self.zeroth_frame):]==0)
+        )
+        subcycle_length_count = np.bincount(ms1_diffs)
+        if np.all(subcycle_length_count[:-1]!=0):
+            raise ValueError("No consistent subcycle length")
+        subcycle_length = len(subcycle_length_count) - 1
+        max_precursor = len(self.fragment_frames.Precursor.unique())
+        subcycle_count = max_precursor // (subcycle_length - 1)
+        frame_count = subcycle_length * subcycle_count
         cycle = np.zeros(
             (
-                frames,
+                frame_count,
                 self.scan_max_index,
                 2,
             )
         )
-        # cycle[:] = -1
-        precursor_frames = np.ones(frames, dtype=np.bool_)
+        precursor_frames = np.ones(frame_count, dtype=np.bool_)
+
+        subframes = self.fragment_frames.drop("Frame", axis=1)
+        for max_index in range(1, len(subframes)):
+            subframe = subframes.iloc[max_index]
+            if subframe.equals(subframes.iloc[0]):
+                break
         for index, row in self.fragment_frames[:max_index].iterrows():
             frame = int(row.Frame - self.zeroth_frame)
             scan_begin = int(row.ScanNumBegin)
             scan_end = int(row.ScanNumEnd)
             low_mz = row.IsolationMz - row.IsolationWidth / 2
             high_mz = row.IsolationMz + row.IsolationWidth / 2
-        #     print(low_mz, high_mz)
             cycle[
                 frame,
                 scan_begin: scan_end,
             ] = (low_mz, high_mz)
             precursor_frames[frame] = False
+
         cycle[precursor_frames] = (-1, -1)
         cycle = cycle.reshape(
             (
-                sub_cycles,
-                frames // sub_cycles,
+                subcycle_count,
+                subcycle_length,
                 *cycle.shape[1:]
             )
         )

misc/bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.3
+current_version = 1.0.4
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

misc/one_click_linux/control

@@ -1,5 +1,5 @@
 Package: AlphaTims
-Version: 1.0.3
+Version: 1.0.4
 Architecture: all
 Maintainer: Mann Labs <[email protected]>
 Description: AlphaTims GUI

misc/one_click_linux/create_installer_linux.sh

@@ -12,7 +12,7 @@ rm -rf dist
 rm -rf build
 python setup.py sdist bdist_wheel
 cd misc/one_click_linux
-pip install "../../dist/alphatims-1.0.3-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.4-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 pip install pyinstaller==4.10
 pyinstaller ../pyinstaller/alphatims.spec -y
 conda deactivate

misc/one_click_macos/Info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphatims.1.0.3</string>
+	<string>alphatims.1.0.4</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.0.3</string>
+	<string>1.0.4</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

misc/one_click_macos/create_installer_macos.sh

@@ -17,7 +17,7 @@ rm -rf build
 python setup.py sdist bdist_wheel
 cd misc/one_click_macos
 pip install pyinstaller==4.10
-pip install "../../dist/alphatims-1.0.3-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.4-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 conda list
 pyinstaller ../pyinstaller/alphatims.spec -y
 conda deactivate
@@ -34,7 +34,7 @@ if false; then
   # https://scriptingosx.com/2019/09/notarize-a-command-line-tool/
   for f in $(find dist/alphatims -name '*.so' -or -name '*.dylib'); do codesign --sign "Developer ID Application: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)" $f; done
   codesign --sign "Developer ID Application: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)" dist/alphatims/Contents/MacOS/alphatims_gui --force --options=runtime --entitlements entitlements.xml
-  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.3 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.4 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   productbuild --distribution distribution.xml --resources Resources --package-path alphatims.pkg dist/alphatims_gui_installer_macos.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   requestUUID=$(xcrun altool --notarize-app --primary-bundle-id "de.mpg.biochem.alphatims.app" --username "[email protected]" --password "@keychain:Alphatims-develop" --asc-provider 7QSY5527AQ --file dist/alphatims_gui_installer_macos.pkg 2>&1 | awk '/RequestUUID/ { print $NF; }')
   request_status="in progress"
@@ -46,6 +46,6 @@ if false; then
   xcrun altool --notarization-info "$requestUUID" --username "[email protected]" --password "@keychain:Alphatims-develop"
   xcrun stapler staple dist/alphatims_gui_installer_macos.pkg
 else
-  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.3 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.4 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg
   productbuild --distribution distribution.xml --resources Resources --package-path alphatims.pkg dist/alphatims_gui_installer_macos.pkg
 fi

misc/one_click_macos/distribution.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>AlphaTims 1.0.3</title>
+    <title>AlphaTims 1.0.4</title>
     <background mime-type="image/png" file="alpha_logo.png" scaling="proportional"/>
     <welcome file="welcome.html" mime-type="text/html" />
     <conclusion file="conclusion.html" mime-type="text/html" />

misc/one_click_windows/alphatims_innoinstaller.iss

@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "AlphaTims"
-#define MyAppVersion "1.0.3"
+#define MyAppVersion "1.0.4"
 #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann department"
 #define MyAppURL "https://github.com/MannLabs/alphatims"
 #define MyAppExeName "alphatims_gui.exe"

misc/one_click_windows/create_installer_windows.bat

@@ -15,7 +15,7 @@ call rmdir dist /s /q
 call rmdir build /s /q
 call python setup.py sdist bdist_wheel
 call cd misc/one_click_windows
-call pip install "../../dist/alphatims-1.0.3-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+call pip install "../../dist/alphatims-1.0.4-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 call pip install pyinstaller==4.10
 call pyinstaller ../pyinstaller/alphatims.spec -y
 call conda deactivate