screamlab 0.1.0__py3-none-any.whl → 0.3.0__py3-none-any.whl

screamlab/dataset.py

@@ -12,6 +12,7 @@ Classes:
 
 """
 
+import sys
 from datetime import datetime
 import numpy as np
 from screamlab import io, utils, settings, functions
@@ -66,6 +67,7 @@ class Dataset:
         print(
             f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S')}: Start buildup fit."
         )
+
         self._start_buildup_fit()
         print(
             f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S')}: "
@@ -86,6 +88,7 @@ class Dataset:
         fitting_type="voigt",
         peak_sign="-",
         line_broadening=None,
+        integration_range=None,
     ):
         """
         Adds a peak to the ds.
@@ -94,7 +97,7 @@ class Dataset:
         ----------
             center_of_peak (float): Peak position in ppm (chemical shift).
             peak_label (str, optional): Custom label. Defaults to "Peak_at_<ppm>_ppm".
-            fitting_type (str, optional): Peak shape: "gauss", "lorentz", or "voigt" (default).
+            fitting_type (str, optional): Peak shape:  "gauss", "lorentz", or "voigt" (default).
             peak_sign (str, optional): "+" for upward, "-" for downward peaks. Defaults to "+".
             line_broadening (dict, optional): Dict with "sigma" and "gamma" keys for line width.
                 Defaults to {"sigma": {"min": 0, "max": 3}, "gamma": {"min": 0, "max": 3}}.
@@ -109,6 +112,7 @@ class Dataset:
         peak.fitting_type = fitting_type
         peak.peak_sign = peak_sign
         peak.line_broadening = line_broadening
+        peak.integration_range = integration_range
 
     def _read_in_data_from_topspin(self):
         """Reads and imports data from TopSpin."""
@@ -132,7 +136,7 @@ class Dataset:
 
     def _calculate_peak_intensities(self):
         """Calculates peak intensities based on fitting methods."""
-        if self.props.prefit:
+        if self.props.prefit and self.props.spectrum_fit_type != "numint":
             print(
                 f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S')}: Start prefit."
             )
@@ -148,7 +152,7 @@ class Dataset:
             result = self.fitter.fit()
             self.lmfit_result_handler.global_fit = result
             self._get_intensities(result)
-        if "global" == self.props.spectrum_fit_type:
+        elif "global" == self.props.spectrum_fit_type:
             print(
                 f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S')}: Start global fit."
             )
@@ -156,6 +160,15 @@ class Dataset:
             result = self.fitter.fit()
             self.lmfit_result_handler.global_fit = result
             self._get_intensities(result)
+        elif "numint" == self.props.spectrum_fit_type:
+            print(
+                f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S')}: Start integration."
+            )
+            self._set_integration_calc()
+            result = self.fitter.fit()
+            self._get_intensities(result)
+        else:
+            sys.exit()
 
     def _start_buildup_fit(self):
         """Performs buildup fitting using the appropriate fitter classes."""
@@ -187,10 +200,18 @@ class Dataset:
         """Sets up a global fitter for all spectra."""
         self.fitter = utils.GlobalFitter(self)
 
+    def _set_integration_calc(self):
+        self.fitter = utils.NumericalIntegration(self)
+
     def _get_intensities(self, result):
         """Extracts intensity values from the fitting results."""
         if isinstance(
-            self.fitter, (utils.IndependentFitter, utils.GlobalFitter)
+            self.fitter,
+            (
+                utils.IndependentFitter,
+                utils.GlobalFitter,
+                utils.NumericalIntegration,
+            ),
         ):
             for peak in self.peak_list:
                 peak.buildup_vals = (result, self.spectra)
@@ -257,6 +278,7 @@ class Peak:
         self._line_broadening = None
         self._line_broadening_init = None
         self._buildup_vals = None
+        self._integration_range = None
 
     def __str__(self):
         """
@@ -264,6 +286,7 @@ class Peak:
 
         :return: A string describing the peak's attributes.
         """
+
         return (
             f"Peak center: {self.peak_center}\n"
             f"Peak label: {self.peak_label}\n"
@@ -277,6 +300,17 @@ class Peak:
             f" {self._format_fitting_range('')}"
         )
 
+    def to_string(self, spectrum_fit_type):
+        if spectrum_fit_type == "numint":
+            return (
+                f"Peak center: {self.peak_center} ppm\n"
+                f"Peak label: {self.peak_label}\n"
+                f"Peak sign: {self.peak_sign}\n"
+                f"Numerical integration range: {self.integration_range} ppm\n"
+            )
+        else:
+            return str(self)
+
     def _format_fitting_range(self, fit_type):
         a_max = "0 and inf" if self.peak_sign == "+" else "-inf and 0"
         lb = ""
@@ -297,6 +331,34 @@ class Peak:
             f"{lb}"
         )
 
+    @property
+    def integration_range(self) -> list:
+        """
+        Gets the integration range.
+
+        :return:
+        """
+        return self._integration_range
+
+    @integration_range.setter
+    def integration_range(self, args):
+        """
+        Sets the integration range.
+
+        :param args: List containing the integration range for numerical integragtion.
+        """
+        if args is not None:
+            if (
+                not isinstance(args, list)
+                or len(args) != 2
+                or not all(isinstance(e, (int, float)) for e in args)
+            ):
+                raise TypeError(
+                    "Integration range must be a list of two numbers or None."
+                )
+
+        self._integration_range = args
+
     @property
     def buildup_vals(self) -> list:
         """
@@ -314,8 +376,14 @@ class Peak:
         :param args: Tuple containing result and spectra.
         """
         result, spectra = args
+
         self._buildup_vals = BuildupList()
-        self._buildup_vals.set_vals(result, spectra, self.peak_label)
+        if isinstance(result, dict):
+            self._buildup_vals.set_num_int_vals(
+                result[self], spectra, self.peak_label
+            )
+        else:
+            self._buildup_vals.set_vals(result, spectra, self.peak_label)
 
     @property
     def line_broadening(self) -> str:
@@ -600,6 +668,21 @@ class BuildupList:
         self._set_intensity(result, label, spectra)
         self._sort_lists()
 
+    def set_num_int_vals(self, result, spectra, label):
+        """
+        Sets buildup values from numerical integration.
+
+        Attributes
+        ----------
+            result (list): Intensity values
+            spectra (list): Spectrum objects used with result to compute buildup.
+            label (str): Peak label used to filter relevant parameters in result.
+
+        """
+        self._set_tpol(spectra)
+        self.intensity = result
+        self._sort_lists()
+
     def _set_tpol(self, spectra):
         self.tpol = [s.tpol for s in spectra]
 

screamlab/io.py

@@ -126,7 +126,7 @@ class ScreamImporter(TopspinImporter):
 
     def _set_number_of_scans(self):
         """Set the number of scans for the last spectrum in the ds."""
-        with open(rf"{self.file}/acqu", "r", encoding="utf-8") as acqu_file:
+        with open(rf"{self.file}/acqus", "r", encoding="utf-8") as acqu_file:
             for acqu_line in acqu_file:
                 if "##$NS=" in acqu_line:
                     self._dataset.spectra[-1].number_of_scans = int(
@@ -258,18 +258,29 @@ class Exporter:
         """
         self._print_report()
         self._plot_topspin_data()
-        self._plot_global_all_together()
-        if self.dataset.props.prefit:
+        if self.dataset.props.spectrum_fit_type != "numint":
+            self._plot_global_all_together()
+        if (
+            self.dataset.props.prefit
+            and self.dataset.props.spectrum_fit_type != "numint"
+        ):
             self._plot_prefit()
             self._print_lmfit_prefit_report()
-        if "global" in self.dataset.props.spectrum_fit_type:
+        if (
+            "global" in self.dataset.props.spectrum_fit_type
+            and self.dataset.props.spectrum_fit_type != "numint"
+        ):
             self._plot_global_each_individual()
-        if "individual" in self.dataset.props.spectrum_fit_type:
+        if (
+            "individual" in self.dataset.props.spectrum_fit_type
+            and self.dataset.props.spectrum_fit_type != "numint"
+        ):
             self._plot_global_each_individual()
         for buildup_type in self.dataset.props.buildup_types:
             self._plot_buildup(buildup_type)
-        self._write_global_fit_results_to_semicolon_separated_file()
-        self._write_buildup_fit_to_semicolon_separated_file()
+        if self.dataset.props.spectrum_fit_type != "numint":
+            self._write_global_fit_results_to_semicolon_separated_file()
+            self._write_buildup_fit_to_semicolon_separated_file()
         self._csv_output()
 
     def _plot_topspin_data(self):
@@ -572,15 +583,22 @@ class Exporter:
             f.write("[[Peaks]]\n")
             for peak_nr, peak in enumerate(self.dataset.peak_list):
                 f.write(f"[Peak {peak_nr + 1}]\n")
-                f.write(str(peak))
+                f.write(peak.to_string(self.dataset.props.spectrum_fit_type))
             f.write("[[Prefit]]\n")
-            if self.dataset.props.prefit:
+            if (
+                self.dataset.props.prefit
+                and self.dataset.props.spectrum_fit_type != "numint"
+            ):
                 self._get_prefit_string(f)
             else:
                 f.write("No prefit performed.\n")
 
-            f.write("[[Global fit results]]\n")
-            self._print_global_fit_results(f)
+            if self.dataset.props.spectrum_fit_type != "numint":
+                f.write("[[Spectral deconvolution results]]\n")
+                self._print_global_fit_results(f)
+            else:
+                f.write("[[Numerical integration results]]\n")
+                self._print_global_fit_results_numint(f)
             f.write("[[Buildup fit results]]\n")
             self._print_buildup(f)
 
@@ -614,6 +632,28 @@ class Exporter:
                     + "\n"
                 )
 
+    def _print_global_fit_results_numint(self, f):
+        header = ["Label", "Time", "Integral"]
+        column_widths = [25, 12, 10]
+        f.write(
+            "".join(f"{h:<{w}}" for h, w in zip(header, column_widths)) + "\n"
+        )
+        for peak_nr, peak in enumerate(self.dataset.peak_list):
+            for integral_nr, integral in enumerate(
+                peak.buildup_vals.intensity
+            ):
+                line = []
+                if integral_nr == 0:
+                    line.append(peak.peak_label)
+                else:
+                    line.append(" ")
+                line.append(peak.buildup_vals.tpol[integral_nr])
+                line.append(round(integral, 4))
+                f.write(
+                    "".join(f"{h:<{w}}" for h, w in zip(line, column_widths))
+                    + "\n"
+                )
+
     def _print_global_fit_results(self, f):
         valdict = screamlab.functions.generate_spectra_param_dict(
             self.dataset.lmfit_result_handler.global_fit.params

screamlab/settings.py

@@ -83,6 +83,8 @@ class Properties:
     def subspec(self, value: Any):
         """Sets list for subspectrum"""
         if value is not None:
+            if len(value) != 2:
+                sys.exit("Error: subspec requires two floats")
             self._subspec = value
         else:
             self._subspec = []
@@ -181,7 +183,7 @@ class Properties:
         """
         str, optional: A list specifying the spectrum fit type
 
-        Options supporded: "global","independent".
+        Options supporded: "global","independent, "numint".
 
         """
         return self._spectrum_fit_type
@@ -189,10 +191,7 @@ class Properties:
     @spectrum_fit_type.setter
     def spectrum_fit_type(self, value: Any):
         """Sets the spectrum fit type"""
-        allowed_values = {
-            "global",
-            "individual",
-        }
+        allowed_values = {"global", "individual", "numint"}
         if not isinstance(value, str):
             raise TypeError(
                 f"Expected 'spectrum_fit_type' to be of type 'str', got"

screamlab/utils.py

@@ -33,7 +33,7 @@ class Fitter:
     """
     Base class for spectral fitting using `lmfit`.
 
-    This class handles parameter initialization and spectral fitting for a ds.
+    This class handles parameter initialization and spectral fitting for a dataset.
 
     Attributes
     ----------
@@ -44,7 +44,7 @@ class Fitter:
 
     def __init__(self, dataset):
         """
-        Initializes the Fitter with a ds.
+        Initializes the Fitter with a dataset.
 
         Args
         ----
@@ -194,8 +194,8 @@ class Fitter:
         return {
             "name": f"{peak.peak_label}_cen_{nr}",
             "value": peak.peak_center,
-            "min": peak.peak_center - 20,
-            "max": peak.peak_center + 20,
+            "min": peak.peak_center - 1,
+            "max": peak.peak_center + 1,
         }
 
     def _get_lw_dict(self, peak, nr, lw):
@@ -281,6 +281,36 @@ class Prefitter(Fitter):
         return result
 
 
+class NumericalIntegration(Fitter):
+
+    def fit(self):
+        integrals = dict()
+        for spectrum in self.dataset.spectra:
+            for peak in self.dataset.peak_list:
+                if peak not in integrals:
+                    integrals[peak] = []
+                self._check_integration_range_in_spectra(spectrum, peak)
+                subspec_x_axis, subspec_y_axis = functions.generate_subspec(
+                    spectrum, peak.integration_range
+                )
+                integrals[peak].append(
+                    np.trapz(subspec_y_axis[::-1], subspec_x_axis[::-1])
+                )
+        return integrals
+
+    def _check_integration_range_in_spectra(self, spectrum, peak):
+        for integration_boundary in peak.integration_range:
+            if not (
+                min(spectrum.x_axis)
+                <= integration_boundary
+                <= max(spectrum.x_axis)
+            ):
+                raise ValueError(
+                    f"Integration boundary {integration_boundary} is outside the spectrum "
+                    f"range ({min(spectrum.x_axis)} – {max(spectrum.x_axis)})."
+                )
+
+
 class GlobalFitter(Fitter):
     """
     Global fit over all spectra at different polarization times.

{screamlab-0.1.0.dist-info → screamlab-0.3.0.dist-info}/METADATA

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: screamlab
-Version: 0.1.0
+Version: 0.3.0
 Summary: Package for reproducible evaluation of SCREAM-DNP data.
 Home-page: https://github.com/FlorianTaube/screamlab
 Author: Florian Taube
 Author-email: florian.taube@uni-rostock.de
 License: BSD
-Project-URL: Documentation, https://github.com/FlorianTaube/screamlab/docs
+Project-URL: Documentation, https://screamlab.readthedocs.io
 Project-URL: Source, https://github.com/FlorianTaube/screamlab/screamlab
 Keywords: Buildup Time Calculator,NMR,DNP,SCREAM_DNP,TopspinExport
 Classifier: Programming Language :: Python :: 3

screamlab-0.3.0.dist-info/RECORD

@@ -0,0 +1,30 @@
+screamlab/__init__.py,sha256=M2vfzk7vI3qvlxE2uIHyGYmPSrFYNUacFjkjiLX00wc,63
+screamlab/dataset.py,sha256=HtWGXm8-M5WFpp_MXHzgKC4lA3G6IUMbGtKgYIMPRzU,25153
+screamlab/functions.py,sha256=vq6YseAt6L0YlduI6LV3_WBcLhFaOqDRGDIIDaZ3kfc,11398
+screamlab/io.py,sha256=Kz-aYxDO9NlADyloxOIFCCmmi0q-jUhFVTMgf9e6L4k,39675
+screamlab/settings.py,sha256=tWcddGbyxXsqvpIc8t9XqGm7XIJXF0QomcG-pIfcfGE,9208
+screamlab/utils.py,sha256=7ndgebGlySfSpCV_M3i3zBNXt_c98XzAWBpO6fmJVfI,26687
+screamlab/__pycache__/__init__.cpython-310.pyc,sha256=nGadfOt1WUjQxMQAWhkaJ8HQIBoFYgJOXOcou6xtrJ4,245
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+screamlab-0.3.0.dist-info/licenses/LICENSE,sha256=Ic_N1IFIdReR7m-W6XtN_4k6B8IgJ33dQFLc6Xi5C2E,1291
+screamlab-0.3.0.dist-info/METADATA,sha256=s_6uhY99C89XRTfLSB5CNgoBRnoOSjSN3fkWz_tu56Q,2942
+screamlab-0.3.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+screamlab-0.3.0.dist-info/top_level.txt,sha256=XjErA4-PG_phESo1eWs-bMzdnBWu4gNxB-RX78zZqqw,10
+screamlab-0.3.0.dist-info/RECORD,,

screamlab-0.1.0.dist-info/RECORD

@@ -1,27 +0,0 @@
-screamlab/__init__.py,sha256=M2vfzk7vI3qvlxE2uIHyGYmPSrFYNUacFjkjiLX00wc,63
-screamlab/dataset.py,sha256=QZSGwm3au08ZEBLdH-pmkyXaeatwBVMZQKs-37j3IQ4,22537
-screamlab/functions.py,sha256=vq6YseAt6L0YlduI6LV3_WBcLhFaOqDRGDIIDaZ3kfc,11398
-screamlab/io.py,sha256=B5I9oxQ4uH2dExnoDlO7Glbk3KcrXSVJcWTEl05eLOk,38017
-screamlab/settings.py,sha256=XBlzWjsdcAO3Fq_d9UyxYViirT9qmpw5_UVrYd-lt0o,9130
-screamlab/utils.py,sha256=VbHaH_QWfcj2WM-TrraPCdjMr7qJ5ybkc2Vgguqhvxg,25503
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