Develop sw

README.md

@@ -20,7 +20,7 @@ AlphaTims is an open-source Python package that provides fast accession and visu
      * [**Installation issues**](#installation-issues)
   * [**Test data**](#test-data)
     * [**Test sample**](#test-sample)
-    * [**LC**](#lc)  
+    * [**LC**](#lc)
     * [**DDA**](#dda)
     * [**DIA**](#dia)
   * [**Usage**](#usage)
@@ -318,6 +318,7 @@ Common installation/usage issues include:
 * **GUI does not open.** In some cases this can be simply because of using an incompatible (default) browser. AlphaTims has been tested with Google Chrome and Mozilla Firefox. Windows IE and Windows Edge compatibility is not guaranteed.
 * **When older Bruker files need to be processed as well,** the [legacy dependencies](requirements/requirements_legacy.txt) are also needed. However, note that this requires [Microsoft Visual C++](https://visualstudio.microsoft.com/visual-cpp-build-tools) to be manually installed (on Windows machines) prior to AlphaTims installation! To include the legacy dependencies, install AlphaTims with `pip install "alphatims[legacy]"` or `pip install "alphatims[legacy]" --upgrade` if already pre-installed.
 * **When installed through `pip`, the GUI cannot be started.** Make sure you install AlphaTims with `pip install "alphatims[plotting-stable]"` to include the GUI with stable dependancies. If this was done and it still fails to run the GUI, a possible fix might be to run `pip install panel==0.10.3` after AlphaTims was installed.
+* **Some external libraries are missing.** On some OS, there might be libraries missing. As an exmaple, the following error message might pop up: `OSError: libgomp.so.1: cannot open shared object file: No such file or directory`. This can be solved by installing those manually, e.g. on Linux: `apt-get install libgomp1`.
 
 ---
 ## How it works

alphatims/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "alphatims"
-__version__ = "1.0.7"
+__version__ = "1.0.8"
 __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

@@ -1982,7 +1982,7 @@ def index_precursors(
         precursor_offsets[-1] = len(precursor_order)
         offset = precursor_offsets[1]
         offsets = precursor_order[offset:]
-        counts = np.empty(len(offsets) + 1, dtype=np.int)
+        counts = np.empty(len(offsets) + 1, dtype=np.int64)
         counts[0] = 0
         counts[1:] = np.cumsum(
             self.quad_indptr[offsets + 1] - self.quad_indptr[offsets]
@@ -2058,22 +2058,23 @@ def index_precursors(
             trimmed_spectrum_intensity_values
         )
 
-    def save_as_mgf(
+    def save_as_spectra(
         self,
         directory: str,
         file_name: str,
         overwrite: bool = False,
         centroiding_window: int = 5,
         keep_n_most_abundant_peaks: int = -1,
+        mgf: bool = True
     ):
-        """Save profile spectra from this TimsTOF object as an mgf file.
+        """Save profile spectra from this TimsTOF object as an spectrum file.
 
         Parameters
         ----------
         directory : str
-            The directory where to save the mgf file.
+            The directory where to save the spectrum file.
         file_name : str
-            The file name of the  mgf file.
+            The file name of the spectrum file.
         overwrite : bool
             If True, an existing file is truncated.
             If False, nothing happens if a file already exists.
@@ -2090,7 +2091,7 @@ def save_as_mgf(
         Returns
         -------
         str
-            The full file name of the mgf file.
+            The full file name of the spectrum file.
         """
         full_file_name = os.path.join(
             directory,
@@ -2127,30 +2128,36 @@ def save_as_mgf(
         mobilities = self.mobility_values[
             self.precursors.ScanNumber.values.astype(np.int64)
         ]
-        with open(full_file_name, "w") as infile:
-            logging.info(f"Exporting profile spectra to {full_file_name}...")
-            for index in alphatims.utils.progress_callback(
-                range(1, self.precursor_max_index)
-            ):
-                start = spectrum_indptr[index]
-                end = spectrum_indptr[index + 1]
-                title = (
-                    f"index: {index}, "
-                    f"intensity: {intensities[index - 1]:.1f}, "
-                    f"mobility: {mobilities[index - 1]:.3f}, "
-                    f"average_mz: {average_mzs[index - 1]:.3f}"
-                )
-                infile.write("BEGIN IONS\n")
-                infile.write(f'TITLE="{title}"\n')
-                infile.write(f"PEPMASS={mono_mzs[index - 1]:.6f}\n")
-                infile.write(f"CHARGE={charges[index - 1]}\n")
-                infile.write(f"RTINSECONDS={rtinseconds[index - 1]:.2f}\n")
-                for mz, intensity in zip(
-                    self.mz_values[spectrum_tof_indices[start: end]],
-                    spectrum_intensity_values[start: end],
-                ):
-                    infile.write(f"{mz:.6f} {intensity}\n")
-                infile.write("END IONS\n")
+        logging.info(f"Exporting profile spectra to {full_file_name}...")
+        if mgf:
+            save_as_mgf(
+                full_file_name,
+                spectrum_indptr,
+                intensities,
+                mobilities,
+                average_mzs,
+                mono_mzs,
+                charges,
+                rtinseconds,
+                spectrum_tof_indices,
+                spectrum_intensity_values,
+                self.precursor_max_index,
+                self.mz_values,
+            )
+        else:
+            save_as_spectra(
+                full_file_name,
+                spectrum_indptr,
+                intensities,
+                mobilities,
+                average_mzs,
+                mono_mzs,
+                charges,
+                rtinseconds,
+                spectrum_tof_indices,
+                spectrum_intensity_values,
+                self.mz_values,
+            )
         logging.info(
             f"Succesfully wrote {self.precursor_max_index - 1:,} "
             f"spectra to {full_file_name}."
@@ -2326,7 +2333,7 @@ class PrecursorFloatError(TypeError):
 
 
 @alphatims.utils.pjit(
-    signature_or_function="void(i8,i8[:],i8[:],i8[:],u4[:],u2[:],u4[:],f8[:],i8[:],i8[:])"
+    # signature_or_function="void(i8,i8[:],i8[:],i8[:],u4[:],u2[:],u4[:],f8[:],i8[:],i8[:])"
 )
 def set_precursor(
     precursor_index: int,
@@ -3291,3 +3298,69 @@ def filter_tof_to_csr(
                 tof_value = tof_indices[idx]
         indptr.append(len(values))
     return np.array(indptr), np.array(values), np.array(columns)
+
+
+def save_as_mgf(
+    full_file_name,
+    spectrum_indptr,
+    intensities,
+    mobilities,
+    average_mzs,
+    mono_mzs,
+    charges,
+    rtinseconds,
+    spectrum_tof_indices,
+    spectrum_intensity_values,
+    precursor_max_index,
+    mz_values,
+):
+    with open(full_file_name, "w") as infile:
+        for index in alphatims.utils.progress_callback(
+            range(1, precursor_max_index)
+        ):
+            start = spectrum_indptr[index]
+            end = spectrum_indptr[index + 1]
+            title = (
+                f"index: {index}, "
+                f"intensity: {intensities[index - 1]:.1f}, "
+                f"mobility: {mobilities[index - 1]:.3f}, "
+                f"average_mz: {average_mzs[index - 1]:.3f}"
+            )
+            infile.write("BEGIN IONS\n")
+            infile.write(f'TITLE="{title}"\n')
+            infile.write(f"PEPMASS={mono_mzs[index - 1]:.6f}\n")
+            infile.write(f"CHARGE={charges[index - 1]}\n")
+            infile.write(f"RTINSECONDS={rtinseconds[index - 1]:.2f}\n")
+            for mz, intensity in zip(
+                mz_values[spectrum_tof_indices[start: end]],
+                spectrum_intensity_values[start: end],
+            ):
+                infile.write(f"{mz:.6f} {intensity}\n")
+            infile.write("END IONS\n")
+
+
+def save_as_spectra(
+    full_file_name,
+    spectrum_indptr,
+    intensities,
+    mobilities,
+    average_mzs,
+    mono_mzs,
+    charges,
+    rtinseconds,
+    spectrum_tof_indices,
+    spectrum_intensity_values,
+    mz_values,
+):
+    with h5py.File(full_file_name, "w") as infile:
+        infile["indptr"] = spectrum_indptr[1:]
+        infile["fragment_mzs"] = mz_values[
+            spectrum_tof_indices
+        ]
+        infile["fragment_intensities"] = spectrum_intensity_values
+        infile["precursor_rt"] = rtinseconds
+        infile["precursor_charge"] = charges
+        infile["precursor_intensity"] = intensities
+        infile["precursor_mobility"] = mobilities
+        infile["precursor_average_mz"] = average_mzs
+        infile["precursor_monoisotopic_mz"] = mono_mzs

alphatims/cli.py

@@ -312,12 +312,46 @@ def export_mgf(**kwargs):
             directory = data.directory
         else:
             directory = parameters["output_folder"]
-        data.save_as_mgf(
+        data.save_as_spectra(
             overwrite=not parameters["disable_overwrite"],
             directory=directory,
             file_name=f"{data.sample_name}.mgf",
             centroiding_window=parameters["centroiding_window"],
-            keep_n_most_abundant_peaks=parameters["keep_n_most_abundant_peaks"]
+            keep_n_most_abundant_peaks=parameters["keep_n_most_abundant_peaks"],
+            mgf=True,
+        )
+
+
+@export.command(
+    "spectra",
+    help="Export BRUKER_RAW_DATA as (profile) spectra file.",
+    no_args_is_help=True,
+)
+@cli_option("bruker_raw_data", as_argument=True)
+@cli_option("keep_n_most_abundant_peaks")
+@cli_option("centroiding_window")
+@cli_option("disable_overwrite")
+@cli_option("output_folder")
+@cli_option("log_file")
+@cli_option("threads")
+@cli_option("disable_log_stream")
+@cli_option("parameter_file")
+@cli_option("export_parameters")
+def export_spectra(**kwargs):
+    with parse_cli_settings("export spectra", **kwargs) as parameters:
+        import alphatims.bruker
+        data = alphatims.bruker.TimsTOF(parameters["bruker_raw_data"])
+        if "output_folder" not in parameters:
+            directory = data.directory
+        else:
+            directory = parameters["output_folder"]
+        data.save_as_spectra(
+            overwrite=not parameters["disable_overwrite"],
+            directory=directory,
+            file_name=f"{data.sample_name}.spectra.hdf",
+            centroiding_window=parameters["centroiding_window"],
+            keep_n_most_abundant_peaks=parameters["keep_n_most_abundant_peaks"],
+            mgf=False,
         )
 
 

misc/bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.7
+current_version = 1.0.8
 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: 1.0.7
+Version: 1.0.8
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 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-1.0.7-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.8-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 pip install pyinstaller==5.6.2
 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.1.0.7</string>
+	<string>alphatims.1.0.8</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.0.7</string>
+	<string>1.0.8</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==5.6.2
-pip install "../../dist/alphatims-1.0.7-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.8-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)" $f; done
   codesign --sign "Developer ID Application: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)" dist/alphatims/Contents/MacOS/alphatims_gui --force --options=runtime --entitlements entitlements.xml
-  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.7 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.8 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   productbuild --distribution distribution.xml --resources Resources --package-path alphatims.pkg dist/alphatims_gui_installer_macos.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   requestUUID=$(xcrun altool --notarize-app --primary-bundle-id "de.mpg.biochem.alphatims.app" --username "willems@biochem.mpg.de" --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 "willems@biochem.mpg.de" --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 1.0.7 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.8 --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 1.0.7</title>
+    <title>AlphaTims 1.0.8</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 "1.0.7"
+#define MyAppVersion "1.0.8"
 #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-1.0.7-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+call pip install "../../dist/alphatims-1.0.8-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 call pip install pyinstaller==4.10
 call pyinstaller ../pyinstaller/alphatims.spec -y
 call conda deactivate

misc/one_click_windows/create_installer_windows.sh

@@ -7,7 +7,7 @@ rm -rf dist
 rm -rf build
 python setup.py sdist bdist_wheel
 cd misc/one_click_windows
-pip install "../../dist/alphatims-1.0.7-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.8-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 pip install pyinstaller==5.6.2
 # TODO https://stackoverflow.com/questions/54175042/python-3-7-anaconda-environment-import-ssl-dll-load-fail-error/60405693#60405693
 pyinstaller ../pyinstaller/alphatims.spec -y