Merge pull request #223 from MannLabs/develop

Develop

alphatims/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "alphatims"
-__version__ = "1.0.0"
+__version__ = "1.0.1"
 __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

@@ -754,6 +754,11 @@ def mobility_values(self):
         """: np.ndarray : np.float64[:] : The mobility values."""
         return self._mobility_values
 
+    @property
+    def cycle(self):
+        """: np.ndarray : np.float64[:,:,:,:] : The quad values."""
+        return self._cycle
+
     @property
     def mz_values(self):
         """: np.ndarray : np.float64[:] : The mz values."""
@@ -1134,6 +1139,14 @@ def _import_data_from_d_folder(
             ) / self.scan_max_index * np.arange(self.scan_max_index)
         mz_min_value = float(self.meta_data["MzAcqRangeLower"])
         mz_max_value = float(self.meta_data["MzAcqRangeUpper"])
+        if self.meta_data["AcquisitionSoftware"] == "Bruker otofControl":
+            logging.warning(
+                "WARNING: Acquisition software is Bruker otofControl, "
+                "mz min/max values are assumed to be 5 m/z wider than "
+                "defined in analysis.tdf!"
+            )
+            mz_min_value -= 5
+            mz_max_value += 5
         tof_intercept = np.sqrt(mz_min_value)
         tof_slope = (
             np.sqrt(mz_max_value) - tof_intercept
@@ -1170,11 +1183,12 @@ def _import_data_from_d_folder(
         self._parse_quad_indptr()
         self._intensity_min_value = int(np.min(self.intensity_values))
         self._intensity_max_value = int(np.max(self.intensity_values))
+        self.set_cycle()
 
     def save_as_hdf(
         self,
-        directory: str,
-        file_name: str,
+        directory: str = None,
+        file_name: str = None,
         overwrite: bool = False,
         compress: bool = False,
         return_as_bytes_io: bool = False,
@@ -1186,9 +1200,11 @@ def save_as_hdf(
         directory : str
             The directory where to save the HDF file.
             Ignored if return_as_bytes_io == True.
+            Default is None, meaning it is parsed from input file.
         file_name : str
             The file name of the  HDF file.
             Ignored if return_as_bytes_io == True.
+            Default is None, meaning it is parsed from input file.
         overwrite : bool
             If True, an existing file is truncated.
             If False, the existing file is appended to only if the original
@@ -1213,6 +1229,10 @@ def save_as_hdf(
             The full file name or a bytes stream containing the HDF file.
         """
         import io
+        if directory is None:
+            directory = self.directory
+        if file_name is None:
+            file_name = f"{self.sample_name}.hdf"
         if overwrite:
             hdf_mode = "w"
         else:
@@ -2250,6 +2270,55 @@ 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.
+        """
+        last_window_group = -1
+        for max_index, (frame, window_group) in enumerate(
+            zip(
+                self.fragment_frames.Frame,
+                self.fragment_frames.Precursor
+            )
+        ):
+            if window_group < last_window_group:
+                break
+            else:
+                last_window_group = window_group
+        frames = self.fragment_frames.Frame[max_index-1]
+        frames += self.fragment_frames.Frame[0] == int(self.zeroth_frame)
+        sub_cycles = frames - len(np.unique(self.fragment_frames.Frame[:max_index]))
+        cycle = np.zeros(
+            (
+                frames,
+                self.scan_max_index,
+                2,
+            )
+        )
+        # cycle[:] = -1
+        precursor_frames = np.ones(frames, dtype=np.bool_)
+        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,
+                *cycle.shape[1:]
+            )
+        )
+        self._cycle = cycle
+
+
 class PrecursorFloatError(TypeError):
     """Used to indicate that a precursor value is not an int but a float."""
     pass

alphatims/plotting.py

@@ -129,8 +129,8 @@ def line_plot(
 
 def heatmap(
     df,
-    x_axis_label: str,
-    y_axis_label: str,
+    x_axis_label: str = "rt",
+    y_axis_label: str = "mobility",
     title: str = "",
     z_axis_label: str = "intensity",
     width: int = 1000,
@@ -150,14 +150,16 @@ def heatmap(
         This should be obtained by slicing an alphatims.bruker.TimsTOF object.
     x_axis_label : str
         A label that is used for projection
-        (i.e. intensities are summed) on the x-axis. Options are:
+        (i.e. intensities are summed) on the x-axis.
+        Default is "rt". Options are:
 
             - mz
             - rt
             - mobility
     y_axis_label : str
         A label that is used for projection
-        (i.e. intensities are summed) on the y-axis. Options are:
+        (i.e. intensities are summed) on the y-axis.
+        Default is "mobility". Options are:
 
             - mz
             - rt

alphatims/tempmmap.py

@@ -59,7 +59,7 @@ def empty(shape: tuple, dtype: np.dtype) -> np.ndarray:
     np.ndarray
         A writable temporary mmapped array.
     """
-    element_count = np.prod(shape)
+    element_count = np.prod(shape, dtype=np.int64)
     if element_count <= 0:
         raise ValueError(
             f"Shape {shape} has an invalid element count of {element_count}"

alphatims/utils.py

@@ -449,6 +449,65 @@ def njit(_func=None, *args, **kwargs):
     return numba.njit(_func, *args, cache=cache, **kwargs)
 
 
+def class_njit(
+    _func=None,
+):
+    import numpy as np
+    import numba
+    import types
+    import ast
+    import textwrap
+    import inspect
+    import pandas as pd
+    def parse_dict(dict_to_parse):
+        result_dict = {}
+        for key, value in dict_to_parse.items():
+            if isinstance(value, pd.DataFrame):
+                key_module = types.ModuleType(f"{key}")
+                for column in value.columns:
+                    key_module.__dict__[column] = np.array(
+                        value[column].values,
+                        copy=False
+                    )
+                result_dict[key] = key_module
+            else:
+                result_dict[key] = value
+        return result_dict
+    def wrapper(func):
+        def inner_func(self, *args, **kwargs):
+            self_ = self
+            self = types.ModuleType(f"{self.__class__}_{id(self)}")
+            self.__dict__.update(parse_dict(self_.__dict__))
+            tree = ast.parse(
+                textwrap.dedent(
+                    inspect.getsource(
+                        func
+                    )
+                )
+            )
+            # tree.body[0].decorator_list = [
+            #     decorator for decorator in tree.body[0].decorator_list if decorator.id != "class_njit"
+            # ]
+            tree.body[0].decorator_list = []
+            tree.body[0].args.args = tree.body[0].args.args[1:]
+            tree.body[0].name = f"{func.__name__}_class_njit"
+            src = ast.unparse(tree)
+            env = dict(locals())
+            env.update(globals())
+            env["numba"] = numba
+            exec(src, env, env)
+            src = f"self_.{func.__name__} = numba.njit(env['{func.__name__}_class_njit'])"
+#             src = f"self_.{func.__name__} = env['{func.__name__}_performance']"
+            exec(src)
+            result = eval(f"self_.{func.__name__}(*args, **kwargs)")
+            return result
+        return inner_func
+    if _func is None:
+        return wrapper
+    else:
+        return wrapper(_func)
+
+
 def pjit(
     _func=None,
     *,

misc/bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.0
+current_version = 1.0.1
 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: 1.0.0
+Version: 1.0.1
 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-1.0.0-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.1-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.1.0.0</string>
+	<string>alphatims.1.0.1</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.0.0</string>
+	<string>1.0.1</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-1.0.0-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.1-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)" $f; done
   codesign --sign "Developer ID Application: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)" dist/alphatims/Contents/MacOS/alphatims_gui --force --options=runtime --entitlements entitlements.xml
-  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.0 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.1 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   productbuild --distribution distribution.xml --resources Resources --package-path alphatims.pkg dist/alphatims_gui_installer_macos.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   requestUUID=$(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 1.0.0 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.1 --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 1.0.0</title>
+    <title>AlphaTims 1.0.1</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 "1.0.0"
+#define MyAppVersion "1.0.1"
 #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-1.0.0-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+call pip install "../../dist/alphatims-1.0.1-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-1.0.0-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.1-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 pip install pyinstaller==4.10
 # TODO https://stackoverflow.com/questions/54175042/python-3-7-anaconda-environment-import-ssl-dll-load-fail-error/60405693#60405693
 pyinstaller ../pyinstaller/alphatims.spec -y