Merge branch 'master' into i70_resolvingpower

Author: wkew

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.3.0
+current_version = 3.4.1
 commit = False
 tag = False
 

README.md

@@ -49,7 +49,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.3.0`
+ `3.4.1`
 
 ***
 
@@ -336,11 +336,11 @@ 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 [3.3.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.3.0), archived on Zenodo:  
+Version [3.4.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.4.1), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg)](https://doi.org/10.5281/zenodo.14009575)
 
-Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.3.0 (Version v3.3.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.4.1 (Version v3.4.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Yuri E. Corilo"
-__version__ = "3.3.0"
+__version__ = "3.4.1"
 import time
 import os
 import sys

corems/mass_spectra/input/rawFileReader.py

@@ -307,6 +307,40 @@ def get_filter_for_scan_num(self, scan_number: int) -> List[str]:
 
         return str(scan_label).split()
 
+    def get_ms_level_for_scan_num(self, scan_number: int) -> str:
+        """
+        Get the MS order for the given scan number.
+
+        Parameters:
+        -----------
+        scan_number : int
+            The scan number
+
+        Returns:
+        --------
+        int
+            The MS order type (1 for MS, 2 for MS2, etc.)
+        """
+        scan_filter = self.iRawDataPlus.GetFilterForScanNumber(scan_number)
+
+        msordertype = {
+            MSOrderType.Ms: 1,
+            MSOrderType.Ms2: 2,
+            MSOrderType.Ms3: 3,
+            MSOrderType.Ms4: 4,
+            MSOrderType.Ms5: 5,
+            MSOrderType.Ms6: 6,
+            MSOrderType.Ms7: 7,
+            MSOrderType.Ms8: 8,
+            MSOrderType.Ms9: 9,
+            MSOrderType.Ms10: 10,
+        }
+
+        if scan_filter.MSOrder in msordertype:
+            return msordertype[scan_filter.MSOrder]
+        else:
+            raise Exception("MS Order Type not found")
+    
     def check_full_scan(self, scan_number: int) -> bool:
         # scan_filter.ScanMode 0 = FULL
         scan_filter = self.iRawDataPlus.GetFilterForScanNumber(scan_number)
@@ -1286,31 +1320,16 @@ def get_scan_df(self):
         # This automatically brings in all the data
         self.chromatogram_settings.scans = (-1, -1)
 
-        # Get scan df info; starting with bulk ms1 and ms2 scans
-        ms1_tic_data, _ = self.get_tic(ms_type="MS", peak_detection=False, smooth=False)
-        ms1_scan_dict = {
-            "scan": ms1_tic_data.scans,
-            "scan_time": ms1_tic_data.time,
-            "tic": ms1_tic_data.tic,
-        }
-        ms1_tic_df = pd.DataFrame.from_dict(ms1_scan_dict)
-        ms1_tic_df["ms_level"] = "ms1"
-
-        ms2_tic_data, _ = self.get_tic(
-            ms_type="MS2", peak_detection=False, smooth=False
-        )
-        ms2_scan_dict = {
-            "scan": ms2_tic_data.scans,
-            "scan_time": ms2_tic_data.time,
-            "tic": ms2_tic_data.tic,
+        # Get scan df info; starting with TIC data
+        tic_data, _ = self.get_tic(ms_type="all", peak_detection=False, smooth=False)
+        tic_data = {
+            "scan": tic_data.scans,
+            "scan_time": tic_data.time,
+            "tic": tic_data.tic,
         }
-        ms2_tic_df = pd.DataFrame.from_dict(ms2_scan_dict)
-        ms2_tic_df["ms_level"] = "ms2"
-
-        scan_df = (
-            pd.concat([ms1_tic_df, ms2_tic_df], axis=0).sort_values(by="scan").reindex()
-        )
-
+        scan_df = pd.DataFrame.from_dict(tic_data)
+        scan_df["ms_level"] = None
+        
         # get scan text
         scan_filter_df = pd.DataFrame.from_dict(
             self.get_all_filters()[0], orient="index"
@@ -1330,11 +1349,11 @@ def get_scan_df(self):
         )
         scan_df["precursor_mz"] = scan_df.scan_text.str.extract(r"(\d+\.\d+)@")
         scan_df["precursor_mz"] = scan_df["precursor_mz"].astype(float)
-        scan_df["ms_level"] = scan_df["ms_level"].str.replace("ms", "").astype(int)
 
-        # Assign each scan as centroid or profile
+        # Assign each scan as centroid or profile and add ms_level
         scan_df["ms_format"] = None
         for i in scan_df.scan.to_list():
+            scan_df.loc[scan_df.scan == i, "ms_level"] = self.get_ms_level_for_scan_num(i)
             if self.iRawDataPlus.IsCentroidScanFromScanNumber(i):
                 scan_df.loc[scan_df.scan == i, "ms_format"] = "centroid"
             else:

docs/corems.html

@@ -154,7 +154,7 @@ <h1 id="corems">CoreMS</h1>
 
 <h2 id="current-version">Current Version</h2>
 
-<p><code>3.3.0</code></p>
+<p><code>3.4.1</code></p>
 
 <hr />
 
@@ -489,11 +489,11 @@ <h2 id="citing-corems">Citing CoreMS</h2>
 
 <p>If you use CoreMS in your work, please use the following citation:</p>
 
-<p>Version <a href="https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.3.0">3.3.0 Release on GitHub</a>, archived on Zenodo:  </p>
+<p>Version <a href="https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.4.1">3.4.1 Release on GitHub</a>, archived on Zenodo:  </p>
 
 <p><a href="https://doi.org/10.5281/zenodo.14009575"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg" alt="DOI" /></a></p>
 
-<p>Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.3.0 (Version v3.3.0), as developed on Github. Zenodo. <a href="http://doi.org/10.5281/zenodo.14009575">http://doi.org/10.5281/zenodo.14009575</a></p>
+<p>Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.4.1 (Version v3.4.1), as developed on Github. Zenodo. <a href="http://doi.org/10.5281/zenodo.14009575">http://doi.org/10.5281/zenodo.14009575</a></p>
 
 <p>```</p>
 
@@ -529,7 +529,7 @@ <h2 id="citing-corems">Citing CoreMS</h2>
                         <label class="view-source-button" for="mod-corems-view-source"><span>View Source</span></label>
 
                         <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Yuri E. Corilo&quot;</span>
-</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;3.3.0&quot;</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;3.4.1&quot;</span>
 </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span> <span class="nn">time</span>
 </span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">import</span> <span class="nn">os</span>
 </span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span> <span class="nn">sys</span>