Add GUI for plotting integrals per package (#26)

* Add GUI for plotting integrals per package

* Fix docstring

* Add `integrals_packages` to documentation

- Fix typos in documentation of special functions

docs/dev/api/guis.rst

@@ -174,6 +174,14 @@ Create a PyQt app and run it.
 
 .. autofunction:: dt_ions
 
+**************************
+:func:`integrals_packages`
+**************************
+
+Create a PyQt app and run it.
+
+.. autofunction:: integrals_packages
+
 *************************
 :func:`nof_ions_per_shot`
 *************************
@@ -202,6 +210,16 @@ Matplotlib PyQt figure to plot histogram for arrival time differences between io
     :members:
     :undoc-members:
 
+****************************
+:class:`IntegralsPerPackage`
+****************************
+
+Matplotlib PyQt figure to integrals per package.
+
+.. autoclass:: IntegralsPerPackage
+    :members:
+    :undoc-members:
+
 ********************
 :class:`IonsPerShot`
 ********************

docs/pkg/special.rst

@@ -30,7 +30,7 @@ The following code shows you how to do this:
 
 .. code-block:: python
 
-    from typing import Path
+    from pathlib import Path
 
     from rimseval import CRDFileProcessor
     from rimseval.guis import hist_nof_shots
@@ -70,7 +70,7 @@ This number is of course user-defined and can be omitted.
 
 .. code-block:: python
 
-    from typing import Path
+    from pathlib import Path
 
     from rimseval import CRDFileProcessor
     from rimseval.guis import dt_ions
@@ -80,3 +80,31 @@ This number is of course user-defined and can be omitted.
     crd.spectrum_full()
 
     dt_ions(crd, max_ns=100)
+
+
+---------------------
+Integrals per package
+---------------------
+
+If you have split your spectrum into packages
+and have defined integrals,
+this routine allows you to show a figure
+of all integrals per package
+versus the number of the package.
+This is especially interesting to find bursts in your measurements,
+i.e., when measuring with the desorption laser.
+
+The following example shows how the plot is generated:
+
+.. code-block:: python
+
+    from pathlib import Path
+
+    from rimseval import CRDFileProcessor
+    from rimseval.guis import integrals_packages
+
+    my_file = Path("path/to/my_file.crd")
+    crd = CRDFileProcessor(crd)
+    crd.spectrum_full()
+
+    integrals_packages(crd)

rimseval/guis/__init__.py

@@ -2,12 +2,13 @@
 
 from .integrals import define_backgrounds_app, define_integrals_app
 from .mcal import create_mass_cal_app
-from .plots import dt_ions, nof_ions_per_shot
+from .plots import dt_ions, integrals_packages, nof_ions_per_shot
 
 __all__ = [
     "create_mass_cal_app",
     "define_backgrounds_app",
     "define_integrals_app",
     "dt_ions",
+    "integrals_packages",
     "nof_ions_per_shot",
 ]

rimseval/guis/plots.py

@@ -1,5 +1,6 @@
 """Plotting capability for specialty functions."""
 
+import itertools
 import sys
 from typing import Tuple
 
@@ -20,6 +21,10 @@
 from rimseval.processor import CRDFileProcessor
 
 
+# markers to cycle through
+MARKERS = ("o", "^", "s", "v", "<", ">", "+", "x", "*", "1", "2", "3", "4")
+
+
 class PlotFigure(QtWidgets.QMainWindow):
     """QMainWindow to plot a Figure."""
 
@@ -157,6 +162,60 @@ def calc_and_draw(self) -> None:
         self.sc.draw()
 
 
+class IntegralsPerPackage(PlotFigure):
+    """Plot integrals of all packages versus package number."""
+
+    def __init__(
+        self, crd: CRDFileProcessor, logy: bool = False, theme: str = None
+    ) -> None:
+        """Initialize the class.
+
+        :param crd: CRD file to process.
+        :param logy: Plot with logarithmic y-axis? Defaults to ``True``
+        :param theme: Theme to plot in, defaults to ``None``.
+
+        :raises OSError: Packages are not defined
+        """
+        super().__init__(logy=logy, theme=theme)
+
+        self.setWindowTitle("Integrals per package")
+
+        self.crd = crd
+
+        if crd.integrals_pkg is None:
+            raise OSError("Integrals for packages are not available.")
+
+        self.calc_and_draw()
+
+    def calc_and_draw(self) -> None:
+        """Create the plot for all the defined integrals."""
+        int_names = self.crd.def_integrals[0]
+        integrals_pkg = self.crd.integrals_pkg
+
+        xdata = np.arange(len(integrals_pkg)) + 1  # start with 1
+        counts = integrals_pkg[:, :, 0]
+        errors = integrals_pkg[:, :, 1]
+
+        # plot
+        marker = itertools.cycle(MARKERS)
+        for it in range(counts.shape[1]):  # loop through all defined integrals
+            dat = counts[:, it]
+            err = errors[:, it]
+            self.axes.errorbar(
+                xdata, dat, yerr=err, ls="--", label=int_names[it], marker=next(marker)
+            )
+
+        # labels
+        self.axes.set_xlabel("Package number")
+        self.axes.set_ylabel("Counts in integral")
+        self.axes.set_title(
+            f"Integrals per package - {self.crd.fname.with_suffix('').name}"
+        )
+        self.axes.legend()
+
+        self.sc.draw()
+
+
 class IonsPerShot(PlotFigure):
     """Plot histogram for number of ions per shot."""
 
@@ -222,6 +281,21 @@ def dt_ions(
     app.exec()
 
 
+def integrals_packages(
+    crd: CRDFileProcessor, logy: bool = False, theme: str = None
+) -> None:
+    """Plot all the integrals versus package number for data split into packages.
+
+    :param crd: CRD file to process.
+    :param logy: Plot with logarithmic y axis? Defaults to ``True``
+    :param theme: Theme to plot in, defaults to ``None``.
+    """
+    app = QtWidgets.QApplication(sys.argv)
+    window = IntegralsPerPackage(crd, logy=logy, theme=theme)
+    window.show()
+    app.exec()
+
+
 def nof_ions_per_shot(
     crd: CRDFileProcessor, logy: bool = False, theme: str = None
 ) -> None: