Major update! Pypi compatible vie 30 ene 2026 12:46:08 CET

Author: DFreireF

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "rionid"
-version = "1.0.0"
+version = "8.0.0"
 description = "Ring-stored ion IDentification: A pure Python tool for Schottky spectrum analysis."
 authors = ["David Freire-Fernández <D.FreireFernandez@gsi.de>"]
 license = "GPL-3.0-or-later"
@@ -9,37 +9,52 @@ homepage = "https://gsi-nuclear-astrophysics.github.io/rionid/"
 repository = "https://github.com/GSI-Nuclear-Astrophysics/rionid"
 keywords = ["Physics", "Nuclear Physics", "Storage Rings", "Mass Spectrometry", "Schottky"]
 
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+
 # Recursively include everything in src/rionid
 packages = [
     { include = "rionid", from = "src" }
 ]
 
-# Ensure mass tables inside the vendorized barion are packaged
-include = [
-    "src/rionid/external/barion/*.mas20",
-    "src/rionid/external/barion/data/*"
-]
+[tool.poetry.urls]
+"Bug Tracker" = "https://github.com/GSI-Nuclear-Astrophysics/rionid/issues"
+"Documentation" = "https://gsi-nuclear-astrophysics.github.io/rionid/"
+"Source Code" = "https://github.com/GSI-Nuclear-Astrophysics/rionid"
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.13"
-numpy = "*"
-scipy = "*"
-PyQt5 = "*"
-pyqtgraph = "*"
-loguru = "*"
-toml = "*"
-ezodf = "*"
-requests = "*"        # Required for Barion to download mass tables
-fortranformat = "*"
+numpy = "^2.0.2"
+scipy = "^1.10.1"
+PyQt5 = "^5.15.9"
+pyqtgraph = "^0.13.3"
+loguru = "^0.7.0"
+toml = "^0.10.2"
+ezodf = "^0.3.2"
+requests = "^2.31.0"        # Required for Barion to download mass tables
+fortranformat = "^2.0.3"
+lxml = "^6.0.2"
+
 [tool.poetry.group.dev.dependencies]
-pytest = "*"
-black = "*"
+pytest = "^8.0.0"
+black = "^25.0.0"
+
+[tool.poetry.group.docs]
+optional = true
+[tool.poetry.group.docs.dependencies]
 # Documentation dependencies
-mkdocs = "*"
-mkdocs-material = "*"
-mkdocstrings = {extras = ["python"], version = "*"}
-mkdocs-gen-files = "*"
-mkdocs-literate-nav = "*"
+mkdocs = "^1.5.0"
+mkdocs-material = "^9.5.0"
+mkdocstrings = {extras = ["python"], version = "^0.24.0"}
+mkdocs-gen-files = "^0.5.0"
+mkdocs-literate-nav = "^0.6.0"
 
 [tool.poetry.scripts]
 rionid = "rionid.gui.app:main"

requirements.txt

@@ -6,4 +6,5 @@ loguru
 toml
 ezodf
 requests
-fortranformat
+fortranformat
+lxml

src/rionid/__init__.py

@@ -1,3 +1,2 @@
 from .core import ImportData
-from .gui.plot import CreatePyGUI
 from .version import __version__

src/rionid/__main__.py

@@ -94,6 +94,9 @@ def main():
             show=args.show,
             app=app
         )
+    
+    if args.show and app:
+        sys.exit(app.exec_())
 
 def run_controller(data_file, particles_to_simulate, alphap, ref_ion, harmonics, 
                    brho=None, fref=None, ke=None, gam=None, correct=None, 
@@ -169,8 +172,6 @@ def run_controller(data_file, particles_to_simulate, alphap, ref_ion, harmonics,
     if show and app:
         sa = CreatePyGUI(mydata.experimental_data, mydata.simulated_data_dict)
         sa.show()
-        # This blocks execution until the window is closed
-        app.exec_()
 
 def display_nions(nions, yield_data, nuclei_names, simulated_data_dict, ref_ion, harmonics):
     """Filters the top N ions by yield."""

src/rionid/core.py

@@ -14,9 +14,7 @@
 from rionid.io import (
     read_psdata, 
     handle_read_tdsm_bin, 
-    handle_read_tdsm, 
-    handle_read_rsa_specan_xml, 
-    handle_spectrumnpz_data, 
+    handle_spectrumnpz_data, # probably I will just keep this option, delete the others
     handle_tiqnpz_data
 )
 from rionid.baseline import NONPARAMS_EST
@@ -72,11 +70,14 @@ def __init__(self, refion, alphap, filename=None, reload_data=None, circumferenc
         self.total_mass = dict()
         self.yield_data = []
 
-        self.ref_ion = refion
         self.highlight_ions = self._parse_highlight_ions(highlight_ions)
         self.alphap = alphap
-        self.gammat = (1/alphap)**0.5 if alphap > 0 else 0
+        self.gammat = 1.0 / (self.alphap ** 0.5)
+
         self.ring = Ring('ESR', circumference)
+
+        self.ref_ion = refion.strip()
+        self._parse_ref_ion(refion)
 
         # Physics / Matching Params
         self.peak_threshold_pct = float(peak_threshold_pct) if peak_threshold_pct else 0.05
@@ -94,6 +95,7 @@ def __init__(self, refion, alphap, filename=None, reload_data=None, circumferenc
         self.match_count = 0
 
         self.cache_file = self._get_cache_file_path(filename) if filename else None
+        self.experimental_data = None
 
         if filename is not None:
             if reload_data:
@@ -102,12 +104,66 @@ def __init__(self, refion, alphap, filename=None, reload_data=None, circumferenc
             else:
                 try:
                     self._load_experimental_data()
-                except FileNotFoundError:
+                except (FileNotFoundError, IOError):
                     self._get_experimental_data(filename)
 
-            # Process peaks after loading
+            # --- NEW DATA PROCESSING BLOCK ---
+            if self.experimental_data is not None:
+                freq, amp = self.experimental_data
+                
+                # 1. Baseline Removal
+                if remove_baseline:
+                    try:
+                        est = NONPARAMS_EST(amp)
+                        baseline = est.pls('BrPLS', l=psd_baseline_removed_l, ratio=1e-6)
+                        amp = amp - baseline
+                    except Exception as e:
+                        print(f"Baseline removal failed: {e}")
+                        traceback.print_exc()
+
+                # 2. Log-Safety (Clip negatives)
+                # Ensure all values are > 0 for logarithmic plotting. 
+                # We use 1e-9 as a "floor" value.
+                amp = np.maximum(amp, 1e-29)
+
+                # 3. Normalization
+                # Scale so the highest peak is 1.0
+                max_val = np.max(amp)
+                if max_val > 0:
+                    amp = amp / max_val
+                
+                # Update the stored data
+                self.experimental_data = (freq, amp)
+            # ---------------------------------
+
+            # Process peaks after loading and processing
             self.detect_peaks_and_widths()
 
+    def _parse_ref_ion(self, refion):
+        # Regex to extract Mass(Digits), Element(Letters), Charge(Digits)
+        # It handles both '98Zr+39' and '98Zr39+' inputs
+        match = re.match(r'(\d+)([a-zA-Z]+).*?(\d+)', self.ref_ion)
+        if match:
+            self.ref_aa = int(match.group(1))
+            self.ref_el = match.group(2)
+            self.ref_charge = int(match.group(3))
+            # Force standard format: 98Zr39+
+            self.ref_ion = f"{self.ref_aa}{self.ref_el}{self.ref_charge}+"
+        else:
+            # Fallback parsing
+            try:
+                # Try splitting by '+' if it exists in the middle
+                if '+' in refion and not refion.endswith('+'):
+                    parts = refion.split('+')
+                    self.ref_charge = int(parts[1])
+                    self.ref_aa = int(re.split(r'(\d+)', parts[0])[1])
+                else:
+                    # Assume format like 98Zr39+
+                    self.ref_charge = int(re.findall(r'\d+', refion)[-1])
+                    self.ref_aa = int(re.findall(r'\d+', refion)[0])
+            except:
+                print(f"Warning: Could not parse reference ion '{refion}'.")
+
     def _parse_highlight_ions(self, input_str):
         """Parses a comma-separated string of ions into a list."""
         if not input_str: return []
@@ -128,15 +184,12 @@ def _get_experimental_data(self, filename):
             self.experimental_data = read_psdata(filename, dbm=False)
         elif ext in ['.bin_fre', '.bin_time', '.bin_amp']:
             self.experimental_data = handle_read_tdsm_bin(filename)
-        elif ext == '.tdms':
-            self.experimental_data = handle_read_tdsm(filename)
-        elif ext in ['.xml', '.specan']:
-            self.experimental_data = handle_read_rsa_specan_xml(filename)
         elif ext == '.npz':
-            if 'spectrum' in base:
-                self.experimental_data = handle_spectrumnpz_data(filename, **self.io_params)
-            else:
-                self.experimental_data = handle_tiqnpz_data(filename, **self.io_params)
+            self.experimental_data = handle_spectrumnpz_data(filename, **self.io_params)
+            #if 'spectrum' in base:
+            #    self.experimental_data = handle_spectrumnpz_data(filename, **self.io_params)
+            #else:
+            #    self.experimental_data = handle_tiqnpz_data(filename, **self.io_params)
         elif ext == '.root':
             raise ValueError("ROOT files are not supported in this version. Please convert to NPZ/CSV.")
 
@@ -166,7 +219,7 @@ def detect_peaks_and_widths(self):
             amp,
             height=height_thresh,
             distance=self.min_distance,
-            prominence=height_thresh * 0.3,
+            prominence=height_thresh * 0.2,
             width=1
         )
 
@@ -257,12 +310,12 @@ def _load_experimental_data(self):
         else:
             raise FileNotFoundError("Cached data file not found. Please set reload_data to True to generate it.")
 
-    def _set_particles_to_simulate_from_file(self, particles_to_simulate, verbose=None):
+    def _set_particles_to_simulate_from_file(self, particles_to_simulate):
         """Parses the LISE++ output file."""
         self.ame = AMEData()
         self.ame_data = self.ame.ame_table
         lise = LISEreader(particles_to_simulate)
-        self.particles_to_simulate = lise.get_info_all(verbose=verbose)
+        self.particles_to_simulate = lise.get_info_all()
 
     def _calculate_moqs(self, particles = None):
         """Calculates mass-to-charge ratios for all particles."""
@@ -299,7 +352,8 @@ def _calculate_srrf(self, fref=None, brho=None, ke=None, gam=None, correct=None)
         self.srrf = array([1 - self.alphap * (self.moq[name] - self.moq[self.ref_ion]) / self.moq[self.ref_ion]
                            for name in self.moq])
         if correct:
-            self.srrf = self.srrf + polyval(array(correct), self.srrf * self.ref_frequency) / self.ref_frequency
+            correction = polyval(array(correct), self.srrf * self.ref_frequency)
+            self.srrf = self.srrf + correction / self.ref_frequency
 
     def _simulated_data(self, brho=None, harmonics=None, mode=None, sim_scalingfactor=None, nions=None):
         """Generates the final simulation dictionary for plotting."""
@@ -328,15 +382,15 @@ def _simulated_data(self, brho=None, harmonics=None, mode=None, sim_scalingfacto
 
         self.nuclei_names = array(moq_keys)
         self.yield_data = np.array(self.yield_data, dtype=float)
+        max_yield = np.max(self.yield_data)
+        if max_yield > 0:
+            self.yield_data /= max_yield
+            
         if sim_scalingfactor:
             self.yield_data *= sim_scalingfactor
 
         for harmonic in harmonics:
-            if mode == 'Frequency':
-                harmonic_freq = self.srrf * self.ref_frequency
-            else:
-                harmonic_freq = self.srrf * self.ref_frequency * harmonic
-            
+            harmonic_freq = self.srrf * self.ref_frequency * harmonic
             arr_stack = stack((harmonic_freq, self.yield_data, self.nuclei_names), axis=1)
             self.simulated_data_dict[f'{harmonic}'] = arr_stack
 

src/rionid/external/lisereader/__init__.py

@@ -1,3 +1,3 @@
-# This copy of Barion is bundled with RionID.
+# This copy of lisereader is bundled with RionID.
 # Original Repository @Github: https://github.com/gwgwhc/lisereader
 # License: GPL-3.0

src/rionid/external/lisereader/reader.py

@@ -2,7 +2,6 @@
 from rionid.external.barion.amedata import AMEData
 from re import sub
 
-
 class LISEreader:
     def __init__(self, filename):
         ame = AMEData()
@@ -108,25 +107,4 @@ def float_check(value): #returns float if not string
         if value.replace('.','').replace('e-','').replace('e+','').isdigit():
             return float(value)
         else:
-            return value
-        
-# ================== testing =====================
-
-def test1():
-    print(f"get_info(\'80Kr\'): {lise_data.get_info('80Kr')}")
-    
-def test2():
-    print(f'get_info_all() snippet[:3]: {lise_data.get_info_all()[:3]}')
-    
-def test3():
-    print(f"get_info_specific([0,1,10]) snippet[:3]: {lise_data.get_info_specific([0,1,10])[:3]}")
-
-if __name__ == '__main__':
-    filename = 'E143_TEline-ESR-72Ge.lpp'
-    lise_data = LISEreader(filename)
-    try:
-        test1()
-        test2()
-        test3()
-    except:
-        raise
+            return value

src/rionid/gui/app.py

@@ -1,5 +1,5 @@
 import sys
-from PyQt5.QtWidgets import (QApplication, QWidget, QVBoxLayout, QSplitter, QDesktopWidget)
+from PyQt5.QtWidgets import (QApplication, QWidget, QVBoxLayout, QSplitter)
 from PyQt5.QtCore import Qt
 import logging as log
 
@@ -31,15 +31,20 @@ def __init__(self):
         super().__init__()
         self.setWindowTitle("RionID")
 
-        # Center and Size Window based on screen resolution
-        width = QDesktopWidget().screenGeometry(-1).width()
-        height = QDesktopWidget().screenGeometry(-1).height()
-        self.setGeometry(100, 100, width, height) 
+        screen = QApplication.primaryScreen()
+        screen_geom = screen.availableGeometry()
+        width = int(screen_geom.width() * 0.8)
+        height = int(screen_geom.height() * 0.8)
+        
+        # Center the window
+        x = (screen_geom.width() - width) // 2
+        y = (screen_geom.height() - height) // 2
+        self.setGeometry(x, y, width, height)   
 
         # Create a QSplitter to hold both the input and the visualization
         splitter = QSplitter(Qt.Horizontal)
 
-        # 1. Create Visualization Widget FIRST
+        # Create Visualization Widget FIRST
         # We must create this first because rion_input needs a reference to it
         # to handle the 'Pick' cursor events.
         self.visualization_widget = CreatePyGUI()