Resolve merge conflicts with master

Author: kheal

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.0.11
+current_version = 2.1.0
 commit = False
 tag = False
 

README.md

@@ -50,7 +50,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.0.11`
+ `2.1.0`
 
 ***
 
@@ -323,7 +323,7 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 If you use CoreMS in your work, please use the following citation:
 
-Version [2.0.11 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.11), archived on Zenodo:  
+Version [2.0.10 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.10), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
 

corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = 'Yuri E. Corilo'
-__version__ = '2.0.11'
+__version__ = '2.1.0'
 __doc__ = '''
 <div align="left">
 
@@ -362,94 +362,6 @@ def __exit__(self, exc_type, exc_val, exc_tb):
         sys.stdout.close()
         sys.stdout = self._original_stdout
 
-def get_filenames(app=None):
-
-    from PySide2.QtCore import Qt, QCoreApplication
-    from PySide2.QtWidgets import QApplication, QFileDialog
-    from pathlib import Path
-
-    app = QApplication(sys.argv)
-    file_dialog = QFileDialog()
-    file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
-    file_location, _ = file_dialog.getOpenFileNames()
-
-    if file_location:
-        QCoreApplication.processEvents()
-        return file_location
-
-    else:
-
-        return None
-
-def get_filename(app=None):
-
-    from PySide2.QtCore import Qt, QCoreApplication
-    from PySide2.QtWidgets import QApplication, QFileDialog
-    from pathlib import Path
-
-    app = QApplication(sys.argv)
-    file_dialog = QFileDialog()
-    file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
-    file_location, _ = file_dialog.getOpenFileName()
-
-    if file_location:
-        QCoreApplication.processEvents()
-        return Path(file_location)
-
-    else:
-
-        return None
-
-def get_dirname(app=None):
-
-    from PySide2.QtCore import Qt, QCoreApplication
-    from PySide2.QtWidgets import QApplication, QFileDialog 
-    from pathlib import Path
-
-    app = QApplication(sys.argv)
-    file_dialog = QFileDialog()
-    file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
-    file_location = file_dialog.getExistingDirectory()
-
-    if file_location:
-        QCoreApplication.processEvents()
-        return Path(file_location)
-
-    else:
-
-        return None
-
-def get_dirnames(app=None):
-
-    from PySide2.QtCore import Qt, QCoreApplication
-    from PySide2.QtWidgets import QApplication, QFileDialog, QTreeView, QListView, QAbstractItemView
-    from pathlib import Path
-
-    if not app:
-        app = QApplication(sys.argv)
-    # file_dialog = QFileDialog()
-    # file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
-    # file_location = file_dialog.getOpenFileNames()
-
-    file_dialog = QFileDialog()
-    file_dialog.setFileMode(QFileDialog.DirectoryOnly)
-    file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
-    file_view = file_dialog.findChild(QListView, 'listView')
-
-    # to make it possible to select multiple directories:
-    if file_view:
-        file_view.setSelectionMode(QAbstractItemView.MultiSelection)
-    f_tree_view = file_dialog.findChild(QTreeView)
-    if f_tree_view:
-        f_tree_view.setSelectionMode(QAbstractItemView.MultiSelection)
-
-    if file_dialog.exec():
-        paths = file_dialog.selectedFiles()
-
-        QCoreApplication.processEvents()
-        for path in paths:
-            yield Path(path)
-
 def chunks(lst, n):
     """Yield successive n-sized chunks from lst."""
     for i in range(0, len(lst), n):
@@ -461,4 +373,4 @@ def corems_md5(fname):
 
     md5_returned = hashlib.sha256(bytes_io).hexdigest()
 
-    return "{}:{}".format("sha256", md5_returned)
+    return "{}:{}".format("sha256", md5_returned)

corems/encapsulation/factory/parameters.py

@@ -1,12 +1,40 @@
+import dataclasses
+
 from corems.encapsulation.factory.processingSetting  import LiquidChromatographSetting, MolecularFormulaSearchSettings, TransientSetting, MassSpecPeakSetting, MassSpectrumSetting
 from corems.encapsulation.factory.processingSetting  import CompoundSearchSettings, GasChromatographSetting
 from corems.encapsulation.factory.processingSetting  import DataInputSetting
 
+def reset_ms_parameters():
+    """Reset the MSParameter class to the default values"""
+    MSParameters.molecular_search = MolecularFormulaSearchSettings()
+    MSParameters.transient = TransientSetting()
+    MSParameters.mass_spectrum = MassSpectrumSetting()
+    MSParameters.ms_peak = MassSpecPeakSetting()
+    MSParameters.data_input = DataInputSetting()
+
+def reset_gcms_parameters():
+    """Reset the GCMSParameters class to the default values"""
+    GCMSParameters.molecular_search = CompoundSearchSettings()
+    GCMSParameters.gc_ms = GasChromatographSetting()
+
+def reset_lcms_parameters():
+    """Reset the LCMSParameters class to the default values"""
+    LCMSParameters.lc_ms = LiquidChromatographSetting()
+    LCMSParameters.mass_spectrum = MassSpectrumSetting()
+    LCMSParameters.ms_peak = MassSpecPeakSetting()
+    LCMSParameters.ms1_molecular_search = MolecularFormulaSearchSettings()
+    LCMSParameters.ms2_molecular_search = MolecularFormulaSearchSettings()
+
 class MSParameters:
     """MSParameters class is used to store the parameters used for the processing of the mass spectrum
     
     Each attibute is a class that contains the parameters for the processing of the mass spectrum, see the corems.encapsulation.factory.processingSetting module for more details.
 
+    Parameters
+    ----------
+    use_defaults: bool, optional
+        if True, the class will be instantiated with the default values, otherwise the current values will be used. Default is False.
+
     Attributes
     -----------
     molecular_search: MolecularFormulaSearchSettings
@@ -19,6 +47,11 @@ class MSParameters:
         MassSpecPeakSetting object
     data_input: DataInputSetting
         DataInputSetting object
+
+    Notes
+    -----
+    One can use the use_defaults parameter to reset the parameters to the default values.
+    Alternatively, to use the current values - modify the class's contents before instantiating the class.
     """
 
     molecular_search = MolecularFormulaSearchSettings()
@@ -27,27 +60,64 @@ class MSParameters:
     ms_peak = MassSpecPeakSetting()
     data_input = DataInputSetting()
 
+    def __init__(self, use_defaults = False) -> None:
+        if not use_defaults:
+            self.molecular_search = dataclasses.replace(MSParameters.molecular_search)
+            self.transient = dataclasses.replace(MSParameters.transient)
+            self.mass_spectrum = dataclasses.replace(MSParameters.mass_spectrum)
+            self.ms_peak = dataclasses.replace(MSParameters.ms_peak)
+            self.data_input = dataclasses.replace(MSParameters.data_input)
+        else:
+            self.molecular_search = MolecularFormulaSearchSettings()
+            self.transient = TransientSetting()
+            self.mass_spectrum = MassSpectrumSetting()
+            self.ms_peak = MassSpecPeakSetting()
+            self.data_input = DataInputSetting()
+
 class GCMSParameters:
     """GCMSParameters class is used to store the parameters used for the processing of the gas chromatograph mass spectrum
 
     Each attibute is a class that contains the parameters for the processing of the data, see the corems.encapsulation.factory.processingSetting module for more details.
 
+    Parameters
+    ----------
+    use_defaults: bool, optional
+        if True, the class will be instantiated with the default values, otherwise the current values will be used. Default is False.
+
     Attributes
     -----------
     molecular_search: MolecularFormulaSearchSettings
         MolecularFormulaSearchSettings object
     gc_ms: GasChromatographSetting
         GasChromatographSetting object
+
+    Notes
+    -----
+    One can use the use_defaults parameter to reset the parameters to the default values.
+    Alternatively, to use the current values - modify the class's contents before instantiating the class.
     """
 
     molecular_search = CompoundSearchSettings()
     gc_ms = GasChromatographSetting()
 
+    def __init__(self, use_defaults = False) -> None:
+        if not use_defaults:
+            self.molecular_search = dataclasses.replace(GCMSParameters.molecular_search)
+            self.gc_ms = dataclasses.replace(GCMSParameters.gc_ms)
+        else:
+            self.molecular_search = CompoundSearchSettings()
+            self.gc_ms = GasChromatographSetting()
+
 class LCMSParameters:
     """LCMSParameters class is used to store the parameters used for the processing of the liquid chromatograph mass spectrum
 
     Each attibute is a class that contains the parameters for the processing of the data, see the corems.encapsulation.factory.processingSetting module for more details.
 
+    Parameters
+    ----------
+    use_defaults: bool, optional
+        if True, the class will be instantiated with the default values, otherwise the current values will be used. Default is False.
+
     Attributes
     -----------
     lc_ms: LiquidChromatographSetting
@@ -60,17 +130,32 @@ class LCMSParameters:
         MolecularFormulaSearchSettings object
     ms2_molecular_search: MolecularFormulaSearchSettings
         MolecularFormulaSearchSettings object
+
+    Notes
+    -----
+    One can use the use_defaults parameter to reset the parameters to the default values.
+    Alternatively, to use the current values - modify the class's contents before instantiating the class.
     """
     lc_ms = LiquidChromatographSetting()
-    
     mass_spectrum = MassSpectrumSetting()
-
     ms_peak = MassSpecPeakSetting()
-
     ms1_molecular_search = MolecularFormulaSearchSettings()
-    
     ms2_molecular_search = MolecularFormulaSearchSettings()
 
+    def __init__(self, use_defaults = False) -> None:
+        if not use_defaults:
+            self.lc_ms = dataclasses.replace(LCMSParameters.lc_ms)
+            self.mass_spectrum = dataclasses.replace(LCMSParameters.mass_spectrum)
+            self.ms_peak = dataclasses.replace(LCMSParameters.ms_peak)
+            self.ms1_molecular_search = dataclasses.replace(LCMSParameters.ms1_molecular_search)
+            self.ms2_molecular_search = dataclasses.replace(LCMSParameters.ms2_molecular_search)
+        else:
+            self.lc_ms = LiquidChromatographSetting()
+            self.mass_spectrum = MassSpectrumSetting()
+            self.ms_peak = MassSpecPeakSetting()
+            self.ms1_molecular_search = MolecularFormulaSearchSettings()
+            self.ms2_molecular_search = MolecularFormulaSearchSettings()
+
 def default_parameters(file_location):  # pragma: no cover
     """Generate parameters dictionary with the default parameters for data processing
        To gather parameters from instrument data during the data parsing step, a parameters dictionary with the default parameters needs to be generated.

corems/mass_spectra/calc/SignalProcessing.py

@@ -4,7 +4,8 @@
 
 from pandas import Series, DataFrame
 
-from scipy.signal import savgol_filter, boxcar
+from scipy.signal import savgol_filter
+from scipy.signal.windows import boxcar
 from scipy import interpolate
 from matplotlib import pyplot as plt
 from numpy import abs