llwp 2.1.3__tar.gz → 2.1.4__tar.gz

llwp-2.1.4/MANIFEST.in

@@ -0,0 +1,4 @@
+include llwp/IconLLWP.svg
+include llwp/IconASAP.svg
+include llwp/IconLLWPMac.png
+include llwp/IconASAPMac.png

{llwp-2.1.3/llwp.egg-info → llwp-2.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: llwp
-Version: 2.1.3
+Version: 2.1.4
 Summary: LLWP is a fast, efficient and easy solution for exploring and assigning spectra - relying on Loomis-Wood plots.
 Author-email: Luis Bonah <bonah@ph1.uni-koeln.de>
 License-Expression: GPL-3.0-only

{llwp-2.1.3 → llwp-2.1.4}/llwp/LLWP.py

@@ -766,11 +766,11 @@ class PlotWidget(QWidget):
             )
 
         if config["convolution_kernel"]:
-            kernel_ys = np.array(config["convolution_kernel"])
+            xmin, xmax = self.xrange
+            kernel_ys = ConvolutionWindow.kernel_at((xmin + xmax) / 2)
             convolution_padding = len(kernel_ys) // 2
             stepwidth = config["convolution_stepwidth"]
 
-            xmin, xmax = self.xrange
             n_xs = (xmax - xmin) // stepwidth + 1
             con_xs = np.arange(-n_xs, n_xs + 1) * stepwidth + (xmax + xmin) / 2
 
@@ -2745,7 +2745,7 @@ class LWPAx:
                     )
 
                 if config["convolution_kernel"]:
-                    kernel_ys = np.array(config["convolution_kernel"])
+                    kernel_ys = ConvolutionWindow.kernel_at((xmin + xmax) / 2)
                     convolution_padding = len(kernel_ys) // 2
                     stepwidth = config["convolution_stepwidth"]
 
@@ -3262,6 +3262,9 @@ class LWPWidget(QGroupBox):
             self.fig.savefig(fname)
 
     def on_click(self, event):
+        if event.canvas.widgetlock.locked():  # Pan or zoom of the matplotlib toolbar is active
+            return
+
         ax = event.inaxes
         index = np.asarray(np.where(self.axes == ax)).T
 
@@ -3908,11 +3911,11 @@ class MainWindow(QMainWindow):
             ]
             for folder in possible_folders:
                 if sys.platform == "darwin":
-                    iconpath = os.path.join(folder, f"{APP_TAG}Mac.png")
+                    iconpath = os.path.join(folder, f"Icon{APP_TAG}Mac.png")
                     if os.path.isfile(iconpath):
                         break
 
-                iconpath = os.path.join(folder, f"{APP_TAG}.svg")
+                iconpath = os.path.join(folder, f"Icon{APP_TAG}.svg")
                 if os.path.isfile(iconpath):
                     break
 
@@ -4231,13 +4234,10 @@ class LLWP(QApplication):
             mainwindow = self.mainwindow_class(self)
             mainwindow.create_gui_components()
 
-            if len(sys.argv) > 1:
-                project = sys.argv[1]
-                if project != "--ASAP":
-                    File.load_files(project)
-
             mainwindow.show()
 
+            self.load_command_line_files()
+
             if messages:
                 notify_warning.emit("\n".join(messages))
 
@@ -4284,6 +4284,28 @@ class LLWP(QApplication):
                     file.color = "#000000"
                     file.apply_color()
 
+    @staticmethod
+    def load_command_line_files():
+        files = []
+        invalid_files = []
+        for argument in sys.argv[1:]:
+            if argument == "--ASAP":
+                continue
+            if os.path.isfile(argument):
+                files.append(os.path.abspath(argument))
+            else:
+                invalid_files.append(argument)
+
+        if invalid_files:
+            invalid_files_string = ", ".join(invalid_files)
+            notify_warning.emit(
+                f"The following command line arguments are not existing and were ignored: {invalid_files_string}"
+            )
+
+        if files:
+            files_by_type = File.sort_files_by_type(files)
+            File.add_multiple_files_by_type(files_by_type)
+
     def run_init_commands(self):
         try:
             commands = config["commandlinedialog_commands"]
@@ -5391,6 +5413,9 @@ class AssignAllDialog(QDialog):
         NewAssignments.get_instance().add_rows(new_assignments)
 
     def on_click(self, event):
+        if event.canvas.widgetlock.locked():  # Pan or zoom of the matplotlib toolbar is active
+            return
+
         clicked_axis = event.inaxes
 
         if not clicked_axis or event.button != 1:
@@ -7374,7 +7399,7 @@ class ConvolutionWindow(EQDockWidget):
     def on_width_changed(self, name, value):
         config["convolution_widths"] = {**config["convolution_widths"], name: value}
 
-    def on_change(self):
+    def compute_kernel(self, frequency=None):
         function = config["convolution_function"]
 
         if function == "Off":
@@ -7401,6 +7426,13 @@ class ConvolutionWindow(EQDockWidget):
                     p.name: config["convolution_widths"].get(p.name, p.default or 1)
                     for p in method.kernel_params()
                 }
+                if method.frequency_dependent_kernel:
+                    if frequency is None:
+                        # Only used to fill the stored kernel, the plots call kernel_at
+                        axes = getattr(mainwindow.lwpwidget, "lwpaxes", None)
+                        axes = [] if axes is None else axes.flatten()
+                        frequency = np.mean(axes[0].xrange) if len(axes) else 0.0
+                    widths["frequency"] = frequency
                 kernel = method(derivative).kernel(kernel_xs, amplitude, **widths)
         else:  # Custom Kernel
             tmp = self.custom_kernel_input.toPlainText().strip()
@@ -7409,7 +7441,23 @@ class ConvolutionWindow(EQDockWidget):
             else:
                 tmp = tmp.split(",")
                 kernel = [float(x) for x in tmp]
+        return kernel
+
+    @classmethod
+    def kernel_at(cls, frequency):
+        """Convolution kernel for a plot centered at `frequency`."""
+        self = cls.instance
+        if config["convolution_kernel"] and config["convolution_function"] not in (
+            "Off",
+            "Custom",
+        ):
+            method = self.get_method()
+            if method is not None and method[0].frequency_dependent_kernel:
+                return np.array(self.compute_kernel(frequency))
+        return np.array(config["convolution_kernel"])
 
+    def on_change(self):
+        kernel = self.compute_kernel()
         config["convolution_kernel"] = list(kernel)
         mainwindow.lwpwidget.set_data()
 
@@ -8270,6 +8318,9 @@ class BlendedLinesWindow(EQDockWidget):
         plot_widget.update_plot_requested.emit()
 
     def add_peak(self, event):
+        if event.canvas.widgetlock.locked():  # Pan or zoom of the matplotlib toolbar is active
+            return
+
         x, y = event.xdata, event.ydata
         is_left_mouse_button = event.button == 1
         if not (x and y and is_left_mouse_button):
@@ -10964,6 +11015,9 @@ class ASAPWidget(LWPWidget):
         mainwindow.statusbar.position_label.setText(text_cursor)
 
     def on_click(self, event):
+        if event.canvas.widgetlock.locked():  # Pan or zoom of the matplotlib toolbar is active
+            return
+
         super().on_click(event)
 
         ax = event.inaxes
@@ -11806,3 +11860,88 @@ if __name__ == "__main__":
 #     return(ts, ys)
 
 # FIDLineshape.postprocessing_function = FID_postprocessing_function
+
+
+## Add Doppler splitted lines to fitting methods
+
+# from llwp.fitmethods import Gauss, Lorentz
+
+# # The splitting is proportional to the frequency. The fitted parameter is the relative
+# # splitting in ppm: the distance of each component from the center at the frequency f is
+# # delta * 1e-6 * f (in the unit of x, e.g. MHz). For 0.05 MHz at 12218 MHz this is 4.1 ppm.
+# START_DELTA = 2.75
+
+
+# def delta_at(frequency, delta):
+#     """Distance of each component from the center at the given frequency."""
+#     return delta * 1e-6 * frequency
+
+
+# # Tick "All Same Width" to use the same relative splitting for all lines.
+# DELTA = Param(
+#     "delta", "Delta (ppm)", shareable=True, default=START_DELTA, in_kernel=True
+# )
+
+
+# class ScaledDoppler(ParametricLineshape):
+#     """Doublet with the components at x0 +- delta_at(x0, delta).
+
+#     The relative splitting is fitted, starting at START_DELTA with bounds 0 and
+#     `max_factor` times that. In the convolution window the relative splitting is entered
+#     by hand (or taken from the last fit). The kernel is created for the frequency at the
+#     center of the plot."""
+
+#     abstract = True
+#     can_convolve = True
+#     frequency_dependent_kernel = True  # kernel() receives the plot's center frequency
+#     component = None  # Lineshape class of the two components
+#     max_factor = 5
+
+#     def __init__(self, derivative=0, **options):
+#         # Start the center of a single fit in the middle of the marked area. The highest
+#         # point is one of the two components and not the center of the doublet.
+#         options.setdefault("xs_weight_factor", 0)
+#         super().__init__(derivative, **options)
+#         self._component = self.component(derivative, **options)
+
+#     def initial_guess(self, guess):
+#         guesses = super().initial_guess(guess)
+#         guesses[-1] = (START_DELTA, 0, self.max_factor * START_DELTA)
+#         return guesses
+
+#     def profile(self, x, *values):
+#         *line, delta = values
+#         x0, amp, *other = line
+#         return self.doublet(x, x0, amp, other, delta_at(x0, delta))
+
+#     def doublet(self, x, x0, amp, other, delta):
+#         return self._component.profile(
+#             x, x0 - delta, amp, *other
+#         ) + self._component.profile(x, x0 + delta, amp, *other)
+
+#     def kernel(self, xs, amplitude, frequency, **widths):
+#         values = []
+#         for param in self.params[:-1]:
+#             if param.role == "center":
+#                 values.append(0)
+#             elif param.role == "amplitude":
+#                 values.append(amplitude)
+#             else:
+#                 values.append(widths.get(param.name, param.default))
+#         delta = delta_at(frequency, widths.get("delta", START_DELTA))
+#         _, amp, *other = values
+#         return self.doublet(xs, 0, amp, other, delta)
+
+
+# class ScaledDopplerGauss(ScaledDoppler):
+#     name = "Doppler Gauss (scaled)"
+#     derivatives = (0, 1, 2)
+#     component = Gauss
+#     params = Gauss.params + (DELTA,)
+
+
+# class ScaledDopplerLorentz(ScaledDoppler):
+#     name = "Doppler Lorentz (scaled)"
+#     derivatives = (0, 1, 2)
+#     component = Lorentz
+#     params = Lorentz.params + (DELTA,)

{llwp-2.1.3 → llwp-2.1.4}/llwp/fitmethods.py

@@ -11,6 +11,8 @@ its menus, depending on which capabilities a class declares:
 * ``can_fit_single``: fits a single line (main axes, assign all, ...)
 * ``can_fit_multi``:  fits several lines at once (Blended Lines window)
 * ``can_convolve``:   can create a kernel to convolute a stick spectrum
+* ``frequency_dependent_kernel``: the kernel depends on the frequency, ``kernel`` then
+                      receives the keyword argument ``frequency`` (center of the plot)
 
 Hierarchy::
 
@@ -174,6 +176,7 @@ class FitMethod:
     can_fit_single = False
     can_fit_multi = False
     can_convolve = False
+    frequency_dependent_kernel = False
     min_points = 2  # Minimum number of data points for a single fit
 
     def __init_subclass__(cls, **kwargs):

{llwp-2.1.3 → llwp-2.1.4/llwp.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: llwp
-Version: 2.1.3
+Version: 2.1.4
 Summary: LLWP is a fast, efficient and easy solution for exploring and assigning spectra - relying on Loomis-Wood plots.
 Author-email: Luis Bonah <bonah@ph1.uni-koeln.de>
 License-Expression: GPL-3.0-only

{llwp-2.1.3 → llwp-2.1.4}/llwp.egg-info/SOURCES.txt

@@ -2,11 +2,11 @@ LICENSE
 MANIFEST.in
 README.md
 pyproject.toml
-llwp/ASAP.svg
-llwp/ASAPMac.png
+llwp/IconASAP.svg
+llwp/IconASAPMac.png
+llwp/IconLLWP.svg
+llwp/IconLLWPMac.png
 llwp/LLWP.py
-llwp/LLWP.svg
-llwp/LLWPMac.png
 llwp/__init__.py
 llwp/__main__.py
 llwp/fitmethods.py

{llwp-2.1.3 → llwp-2.1.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "llwp"
-version = "2.1.3"
+version = "2.1.4"
 authors = [
   { name="Luis Bonah", email="bonah@ph1.uni-koeln.de" },
 ]

llwp-2.1.3/MANIFEST.in

@@ -1,4 +0,0 @@
-include llwp/LLWP.svg
-include llwp/ASAP.svg
-include llwp/LLWPMac.png
-include llwp/ASAPMac.png