ms-mint 0.2.2__tar.gz → 0.2.4__tar.gz

{ms-mint-0.2.2/ms_mint.egg-info → ms-mint-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ms-mint
-Version: 0.2.2
+Version: 0.2.4
 Summary: Metabolomics Integrator (Mint)
 Home-page: https://github.com/LewisResearchGroup/ms-mint
 Author: Soren Wacker
@@ -26,7 +26,7 @@ The `ms-mint` library includes a range of functions for processing LCMS data fro
 ## Documentation
 The code documentation can be accessed [here](https://lewisresearchgroup.github.io/ms-mint/readme.html).
 
-## News
+## ms-mint application with graphical user iterface (GUI)
 MINT has been split into the Python library and the app. This repository contains the Python library. For the app follow [this link](https://github.com/LewisResearchGroup/ms-mint-app).
 
 ## Contributions
@@ -38,7 +38,7 @@ The project follows PEP8 standard and uses Black and Flake8 to ensure a consiste
 
 ---
 
-# Usage
+## Usage
 
 To use the main class of the ms-mint library, you can import it into your code with the following command:
 
@@ -159,7 +159,6 @@ Then we apply the changes and plot the new peak shapes:
 
 As you can see, the shapes of Xanthine, Succinate, Citrulline look much better.
 
-
 ## Plotting and data exploration
 
 The `Mint` class has a few convenient methods to visualize and explore the processed data. The results can be viewed directly in JupyterLab or stored to files using `matplotlib` and `seaborn` syntax. The figures are matplotlib objects and can be easily customised. 
@@ -172,7 +171,6 @@ The `Mint` class has a few convenient methods to visualize and explore the proce
 
 The method uses seaborn [sns.relplot()](https://seaborn.pydata.org/generated/seaborn.relplot.html) function and keyword arguments are passed on. 
 
-
 ## Hierarchical clustering
 Mint ca be used to cluster the extracted data. An agglomerative hierarchical clustering is a bottom-up clustering technique where each data point starts as its own cluster and then are merged with other clusters in a hierarchical manner based on their proximity or similarity until a single cluster is formed or a specified stopping criteria is met. The proximity is usually determined by a distance metric, such as Euclidean distance, and the similarity is usually determined by a linkage function, such as ward linkage or complete linkage. The result is a tree-like representation called a dendrogram, which can be used to determine the number of clusters and the cluster assignments of the data points.
 
@@ -202,7 +200,6 @@ Before clustering the data can be transformed and scaled. By default `log2p1(x)
         cmap=None  # Name of a matplotlib color map                
     )
 
-
 ![](notebooks/hierarchical_clustering.png)
 
 ## Principal Components Analysis
@@ -219,8 +216,8 @@ After running the PCA the results can be plotted with:
     
 ![](notebooks/pca-pairplot.png)
 
-# FAQ
-## What is a target list
+## FAQ
+### What is a target list
 A target list is a pandas dataframe with specific columns. 
 
 -   **peak_label**: string, Label of the peak (must be unique).
@@ -235,11 +232,11 @@ A target list is a pandas dataframe with specific columns.
 
 The target list can be stored as csv or Excel file. 
 
-## What input files can be used
+### What input files can be used
 `ms_mint` can be used with `mzXML`, `mzML`, `mzMLb` and experimental formats in `.feather` and `.parquet` format.
 
-## Which properties does ms-mint extract
-### Parameters from target list
+### Which properties does ms-mint extract
+#### Parameters from target list
 -   **ms_file**: Filename of MS-file
 -   **peak_label**: From target list
 -   **mz_mean**: From target list
@@ -253,7 +250,7 @@ The target list can be stored as csv or Excel file.
 
 ---
 
-### Results columns
+#### Results columns
 -   **peak_area**: The sum of all intensities in the extraction window
 -   **peak_area_top3**: The average of the 3 largest intensities in the extraction window
 -   **peak_n_datapoints**: Number of datapoints
@@ -274,9 +271,7 @@ The target list can be stored as csv or Excel file.
 -   **ms_file_size**: Size of the MS-file in MB
 ---
 
+## Release Notes
 
-# Release Notes
-
-## 0.2.0 Milestones
+### 0.2.0 Milestones
     - peak_area_top3 comparable to El-Maven PeakAreaTop values
-

{ms-mint-0.2.2 → ms-mint-0.2.4}/README.md

@@ -12,7 +12,7 @@ The `ms-mint` library includes a range of functions for processing LCMS data fro
 ## Documentation
 The code documentation can be accessed [here](https://lewisresearchgroup.github.io/ms-mint/readme.html).
 
-## News
+## ms-mint application with graphical user iterface (GUI)
 MINT has been split into the Python library and the app. This repository contains the Python library. For the app follow [this link](https://github.com/LewisResearchGroup/ms-mint-app).
 
 ## Contributions
@@ -24,7 +24,7 @@ The project follows PEP8 standard and uses Black and Flake8 to ensure a consiste
 
 ---
 
-# Usage
+## Usage
 
 To use the main class of the ms-mint library, you can import it into your code with the following command:
 
@@ -145,7 +145,6 @@ Then we apply the changes and plot the new peak shapes:
 
 As you can see, the shapes of Xanthine, Succinate, Citrulline look much better.
 
-
 ## Plotting and data exploration
 
 The `Mint` class has a few convenient methods to visualize and explore the processed data. The results can be viewed directly in JupyterLab or stored to files using `matplotlib` and `seaborn` syntax. The figures are matplotlib objects and can be easily customised. 
@@ -158,7 +157,6 @@ The `Mint` class has a few convenient methods to visualize and explore the proce
 
 The method uses seaborn [sns.relplot()](https://seaborn.pydata.org/generated/seaborn.relplot.html) function and keyword arguments are passed on. 
 
-
 ## Hierarchical clustering
 Mint ca be used to cluster the extracted data. An agglomerative hierarchical clustering is a bottom-up clustering technique where each data point starts as its own cluster and then are merged with other clusters in a hierarchical manner based on their proximity or similarity until a single cluster is formed or a specified stopping criteria is met. The proximity is usually determined by a distance metric, such as Euclidean distance, and the similarity is usually determined by a linkage function, such as ward linkage or complete linkage. The result is a tree-like representation called a dendrogram, which can be used to determine the number of clusters and the cluster assignments of the data points.
 
@@ -188,7 +186,6 @@ Before clustering the data can be transformed and scaled. By default `log2p1(x)
         cmap=None  # Name of a matplotlib color map                
     )
 
-
 ![](notebooks/hierarchical_clustering.png)
 
 ## Principal Components Analysis
@@ -205,8 +202,8 @@ After running the PCA the results can be plotted with:
     
 ![](notebooks/pca-pairplot.png)
 
-# FAQ
-## What is a target list
+## FAQ
+### What is a target list
 A target list is a pandas dataframe with specific columns. 
 
 -   **peak_label**: string, Label of the peak (must be unique).
@@ -221,11 +218,11 @@ A target list is a pandas dataframe with specific columns.
 
 The target list can be stored as csv or Excel file. 
 
-## What input files can be used
+### What input files can be used
 `ms_mint` can be used with `mzXML`, `mzML`, `mzMLb` and experimental formats in `.feather` and `.parquet` format.
 
-## Which properties does ms-mint extract
-### Parameters from target list
+### Which properties does ms-mint extract
+#### Parameters from target list
 -   **ms_file**: Filename of MS-file
 -   **peak_label**: From target list
 -   **mz_mean**: From target list
@@ -239,7 +236,7 @@ The target list can be stored as csv or Excel file.
 
 ---
 
-### Results columns
+#### Results columns
 -   **peak_area**: The sum of all intensities in the extraction window
 -   **peak_area_top3**: The average of the 3 largest intensities in the extraction window
 -   **peak_n_datapoints**: Number of datapoints
@@ -260,9 +257,7 @@ The target list can be stored as csv or Excel file.
 -   **ms_file_size**: Size of the MS-file in MB
 ---
 
+## Release Notes
 
-# Release Notes
-
-## 0.2.0 Milestones
+### 0.2.0 Milestones
     - peak_area_top3 comparable to El-Maven PeakAreaTop values
-

{ms-mint-0.2.2 → ms-mint-0.2.4}/ms_mint/Mint.py

@@ -22,7 +22,8 @@ from .tools import (
 )
 from .pca import PrincipalComponentsAnalyser
 from .plotting import MintPlotter
-#from .filter import Resampler
+
+# from .filter import Resampler
 from .chromatogram import Chromatogram, extract_chromatogram_from_ms1
 
 import ms_mint
@@ -45,11 +46,15 @@ class Mint(object):
 
     """
 
-    def __init__(self, verbose: bool = False, progress_callback=None, time_unit="s"):
-
-        self._verbose = verbose
+    def __init__(
+        self,
+        verbose: bool = False,
+        progress_callback: Callable = None,
+        time_unit: str = "s",
+    ):
+        self.verbose = verbose
         self._version = ms_mint.__version__
-        self._progress_callback = progress_callback
+        self.progress_callback = progress_callback
         self.reset()
         if self.verbose:
             print("Mint Version:", self.version, "\n")
@@ -59,24 +64,6 @@ class Mint(object):
         self.tqdm = tqdm
         self.meta = None
 
-    @property
-    def verbose(self):
-        """
-        Get/set verbosity.
-
-        :getter: Get current verbosity.
-        :return: True or False
-        :rtype: bool
-        :setter: Sets verbosity.
-        :param value: True or False
-        :type value: bool
-        """
-        return self._verbose
-
-    @verbose.setter
-    def verbose(self, value: bool):
-        self._verbose = value
-
     @property
     def version(self):
         """
@@ -133,11 +120,11 @@ class Mint(object):
                 * 1: Run without multiprocessing on one CPU
                 * >1: Run with multiprocessing enabled using nthreads threads.
         :param mode: Compute mode ('standard' or 'express'), defaults to 'standard'
+        :type mode: str
                 * 'standard': calculates peak shaped projected to RT dimension
                 * 'express': omits calculation of other features, only peak_areas
         :param fn: Output filename to not keep results in memory.
         :type fn: str
-        :type mode: str
         :param kwargs: Arguments passed to the procesing function.
         """
         self._status = "running"
@@ -146,39 +133,57 @@ class Mint(object):
             return None
 
         targets = self.targets.reset_index()
+        self._set_rt_min_max(targets, rt_margin)
 
-        if "rt" in targets.columns:
-            ndx = (targets.rt_min.isna()) & (~targets.rt.isna())
-            targets.loc[ndx, "rt_min"] = targets.loc[ndx, "rt"] - rt_margin
-            ndx = (targets.rt_max.isna()) & (~targets.rt.isna())
-            targets.loc[ndx, "rt_max"] = targets.loc[ndx, "rt"] + rt_margin
-            del ndx
-
-        if nthreads is None:
-            nthreads = min(cpu_count(), self.n_files)
+        nthreads = self._determine_nthreads(nthreads)
 
         if self.verbose:
             print(f"Run MINT with {nthreads} processes:")
 
         start = time.time()
         if nthreads > 1:
-            self.__run_parallel__(nthreads=nthreads, mode=mode, fn=fn, **kwargs)
+            self._run_parallel(nthreads=nthreads, mode=mode, fn=fn, **kwargs)
         else:
-            results = []
-            for i, filename in enumerate(self.ms_files):
-                args = {
-                    "filename": filename,
-                    "targets": targets,
-                    "q": None,
-                    "mode": mode,
-                    "output_fn": None,
-                }
-                results.append(process_ms1_files_in_parallel(args))
-                self.progress = int(100 * (i / self.n_files))
-            self.results = pd.concat(results).reset_index(drop=True)
+            self._run_sequential(mode=mode, fn=fn, targets=targets)
 
         self.progress = 100
+        self._report_runtime(start)
+
+        self._status = "done"
+        assert self.progress == 100
+        return self
 
+    def _set_rt_min_max(self, targets, rt_margin):
+        if "rt" in targets.columns:
+            update_rt_min = (targets.rt_min.isna()) & (~targets.rt.isna())
+            targets.loc[update_rt_min, "rt_min"] = (
+                targets.loc[update_rt_min, "rt"] - rt_margin
+            )
+            update_rt_max = (targets.rt_max.isna()) & (~targets.rt.isna())
+            targets.loc[update_rt_max, "rt_max"] = (
+                targets.loc[update_rt_max, "rt"] + rt_margin
+            )
+
+    def _determine_nthreads(self, nthreads):
+        if nthreads is None:
+            nthreads = min(cpu_count(), self.n_files)
+        return nthreads
+
+    def _run_sequential(self, mode, fn, targets):
+        results = []
+        for i, filename in enumerate(self.ms_files):
+            args = {
+                "filename": filename,
+                "targets": targets,
+                "q": None,
+                "mode": mode,
+                "output_fn": None,
+            }
+            results.append(process_ms1_files_in_parallel(args))
+            self.progress = int(100 * (i / self.n_files))
+        self.results = pd.concat(results).reset_index(drop=True)
+
+    def _report_runtime(self, start):
         end = time.time()
         self.runtime = end - start
         self.runtime_per_file = self.runtime / self.n_files
@@ -192,11 +197,7 @@ class Mint(object):
             )
             print("Results:", self.results)
 
-        self._status = "done"
-        assert self.progress == 100
-        return self
-
-    def __run_parallel__(
+    def _run_parallel(
         self, nthreads=1, mode="standard", maxtasksperchild=None, fn=None
     ):
         print(f"maxtasksperchild: {maxtasksperchild}")
@@ -221,17 +222,7 @@ class Mint(object):
             )
 
         results = pool.map_async(process_ms1_files_in_parallel, args)
-
-        # monitor progress
-        while True:
-            if results.ready():
-                break
-            else:
-                size = q.qsize()
-                self.progress = 100 * size / self.n_files
-                time.sleep(1)
-
-        self.progress = 100
+        self._monitor_progress(results, q)
 
         pool.close()
         pool.join()
@@ -240,6 +231,13 @@ class Mint(object):
             results = results.get()
             self.results = pd.concat(results).reset_index(drop=True)
 
+    def _monitor_progress(self, results, q):
+        while not results.ready():
+            size = q.qsize()
+            self.progress = 100 * size / self.n_files
+            time.sleep(1)
+        self.progress = 100
+
     @property
     def status(self):
         """
@@ -398,20 +396,6 @@ class Mint(object):
             df = scale_dataframe(df, scaler=scaler)
         return df
 
-    @property
-    def progress_callback(self):
-        """
-        Assigns a callback function to update a progress bar.
-
-        :getter: Returns the current callback function.
-        :setter: Sets the callback function.
-        """
-        return self._progress_callback
-
-    @progress_callback.setter
-    def progress_callback(self, func: Callable = None):
-        self._progress_callback = func
-
     @property
     def progress(self):
         """
@@ -501,7 +485,7 @@ class Mint(object):
             peak_label = self.peak_labels
 
         data = []
-        
+
         for fn in self.tqdm(fns):
             df = ms_file_to_df(fn)
             for label in peak_label:
@@ -517,7 +501,7 @@ class Mint(object):
                 chrom_data["ms_file"] = fn
                 chrom_data["peak_label"] = label
                 chrom_data["rt_min"] = rt_min
-                chrom_data["rt_max"] = rt_min
+                chrom_data["rt_max"] = rt_max
                 data.append(chrom_data)
 
         data = pd.concat(data).reset_index()

{ms-mint-0.2.2 → ms-mint-0.2.4}/ms_mint/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-03-09T14:53:52-0700",
+ "date": "2023-05-09T10:35:26-0600",
  "dirty": false,
  "error": null,
- "full-revisionid": "7107a0d99427edc8f89ec5853dcef4dddff9c839",
- "version": "v0.2.2"
+ "full-revisionid": "509e8d0641ce628f2c4e4fdf65a850d805427c99",
+ "version": "v0.2.4"
 }
 '''  # END VERSION_JSON
 

{ms-mint-0.2.2 → ms-mint-0.2.4}/ms_mint/chromatogram.py

@@ -6,13 +6,13 @@ from matplotlib import pyplot as plt
 
 from .tools import find_peaks_in_timeseries, gaussian, mz_mean_width_to_min_max
 from .io import ms_file_to_df
-from .filter import Resampler, Smoother, GaussFilter
+from .filters import Resampler, Smoother, GaussFilter
 from .matplotlib_tools import plot_peaks
 
 
 class Chromatogram:
     def __init__(
-        self, scan_times=None, intensities=None, filter=None, expected_rt=None
+        self, scan_times=None, intensities=None, filters=None, expected_rt=None
     ):
         self.t = np.array([0])
         self.x = np.array([0])
@@ -21,10 +21,10 @@ class Chromatogram:
         if intensities is not None:
             self.x = np.append(self.x, intensities)
         self.noise_level = None
-        if filter is None:
-            self.filter = [Resampler(), GaussFilter(), Smoother()]
+        if filters is None:
+            self.filters = [Resampler(), GaussFilter(), Smoother()]
         else:
-            self.filter = filter
+            self.filters = filters
         self.peaks = None
         self.selected_peak_ndxs = None
         if expected_rt is None and scan_times is not None:
@@ -43,8 +43,8 @@ class Chromatogram:
         data = pd.Series(index=self.t, data=self.x)
         self.noise_level = data.rolling(window, center=True).std().median()
 
-    def apply_filter(self):
-        for filt in self.filter:
+    def apply_filters(self):
+        for filt in self.filters:
             self.t, self.x = filt.transform(self.t, self.x)
 
     def find_peaks(self, prominence=None, rel_height=0.9):
@@ -80,7 +80,6 @@ class Chromatogram:
             plt.show()
 
         for ndx, row in peaks.iterrows():
-
             new_rt_min = row.rt_min
             new_rt_max = row.rt_max
 
@@ -130,7 +129,7 @@ class Chromatogram:
 
     @property
     def selected_peaks(self):
-        self.peaks.loc[self.selected_peak_ndxs]
+        return self.peaks.loc[self.selected_peak_ndxs]
 
     @property
     def data(self):

{ms-mint-0.2.2 → ms-mint-0.2.4}/ms_mint/filelock.py

@@ -50,15 +50,6 @@ try:
 except ImportError:
     fcntl = None
 
-
-# Backward compatibility
-# ------------------------------------------------
-try:
-    TimeoutError
-except NameError:
-    TimeoutError = OSError
-
-
 # Data
 # ------------------------------------------------
 __all__ = [
@@ -105,6 +96,7 @@ class Timeout(TimeoutError):
 # Classes
 # ------------------------------------------------
 
+
 # This is a helper class which is returned by :meth:`BaseFileLock.acquire`
 # and wraps the lock to make sure __enter__ is not called twice when entering
 # the with statement.
@@ -310,7 +302,6 @@ class BaseFileLock(object):
             every case.
         """
         with self._thread_lock:
-
             if self.is_locked:
                 self._lock_counter -= 1
 

ms-mint-0.2.2/ms_mint/filter.py → ms-mint-0.2.4/ms_mint/filters.py

@@ -49,7 +49,7 @@ class Smoother:
     averages.
     """
 
-    def __init__(self, windows=[30, 20]):
+    def __init__(self, windows=None):
         """
         Filter for time series that smoothes the
         x values by running one or more rolling
@@ -58,6 +58,8 @@ class Smoother:
         :param windows: Window sizes of rolling averages applied to time series, defaults to [30, 20]
         :type windows: : List[int], optional
         """
+        if windows is None:
+            windows = [30, 20]
         self.windows = windows
         self.name = "smoother"