From 1cbfd36a63c79a44f90fd527e0146c50a8a58b02 Mon Sep 17 00:00:00 2001
From: rettigl <l.rettig@web.de>
Date: Tue, 15 Oct 2024 21:26:01 +0200
Subject: [PATCH 1/7] adopt figure sizes

---
 src/sed/calibrator/energy.py   | 19 ++++++++++++-------
 src/sed/calibrator/momentum.py |  5 ++---
 src/sed/core/processor.py      |  4 ++--
 src/sed/diagnostics.py         |  2 +-
 4 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/src/sed/calibrator/energy.py b/src/sed/calibrator/energy.py
index 65493f66..7f1426f9 100644
--- a/src/sed/calibrator/energy.py
+++ b/src/sed/calibrator/energy.py
@@ -351,7 +351,7 @@ def adjust_ranges(
 
         # make plot
         labels = kwds.pop("labels", [str(b) + " V" for b in self.biases])
-        figsize = kwds.pop("figsize", (8, 4))
+        figsize = kwds.pop("figsize", (6, 4))
         plot_segs = []
         plot_peaks = []
         fig, ax = plt.subplots(figsize=figsize)
@@ -664,15 +664,19 @@ def view(
 
         sign = 1 if energy_scale == "kinetic" else -1
 
+        figsize = kwds.pop("figsize", (6, 4))
+
         if backend == "matplotlib":
-            figsize = kwds.pop("figsize", (6, 4))
+            colors = plt.get_cmap("rainbow")(np.linspace(0, 1, len(traces)))
             fig_plt, ax = plt.subplots(figsize=figsize)
-            for itr, trace in enumerate(traces):
+            for itr, color in zip(range(len(traces)), colors):
+                trace = traces[itr, :]
                 if align:
                     ax.plot(
                         xaxis + sign * (self.biases[itr]),
                         trace,
                         ls="-",
+                        color=color,
                         linewidth=1,
                         label=lbs[itr],
                         **linekwds,
@@ -682,6 +686,7 @@ def view(
                         xaxis,
                         trace,
                         ls="-",
+                        color=color,
                         linewidth=1,
                         label=lbs[itr],
                         **linekwds,
@@ -696,6 +701,7 @@ def view(
                         tofseg,
                         traceseg,
                         ls="-",
+                        color=color,
                         linewidth=2,
                         **linesegkwds,
                     )
@@ -710,7 +716,7 @@ def view(
 
             if show_legend:
                 try:
-                    ax.legend(fontsize=12, **legkwds)
+                    ax.legend(fontsize=8, loc="upper right", **legkwds)
                 except TypeError:
                     pass
 
@@ -721,11 +727,10 @@ def view(
             colors = it.cycle(ColorCycle[10])
             ttp = [("(x, y)", "($x, $y)")]
 
-            figsize = kwds.pop("figsize", (800, 300))
             fig = pbk.figure(
                 title=ttl,
-                width=figsize[0],
-                height=figsize[1],
+                width=figsize[0] * 100,
+                height=figsize[1] * 100,
                 tooltips=ttp,
             )
             # Plotting the main traces
diff --git a/src/sed/calibrator/momentum.py b/src/sed/calibrator/momentum.py
index 33047292..36a41b86 100644
--- a/src/sed/calibrator/momentum.py
+++ b/src/sed/calibrator/momentum.py
@@ -1393,11 +1393,10 @@ def view(
             output_notebook(hide_banner=True)
             colors = it.cycle(ColorCycle[10])
             ttp = [("(x, y)", "($x, $y)")]
-            figsize = kwds.pop("figsize", (320, 300))
             palette = cm2palette(cmap)  # Retrieve palette colors
             fig = pbk.figure(
-                width=figsize[0],
-                height=figsize[1],
+                width=figsize[0] * 100,
+                height=figsize[1] * 100,
                 tooltips=ttp,
                 x_range=(0, num_rows),
                 y_range=(0, num_cols),
diff --git a/src/sed/core/processor.py b/src/sed/core/processor.py
index f40089bb..b23dfa74 100644
--- a/src/sed/core/processor.py
+++ b/src/sed/core/processor.py
@@ -1243,7 +1243,7 @@ def load_bias_series(
         self.ec.view(
             traces=self.ec.traces_normed,
             xaxis=self.ec.tof,
-            backend="bokeh",
+            backend="matplotlib",
         )
 
     # 2. extract ranges and get peak positions
@@ -1303,7 +1303,7 @@ def find_bias_peaks(
                     segs=self.ec.featranges,
                     xaxis=self.ec.tof,
                     peaks=self.ec.peaks,
-                    backend="bokeh",
+                    backend="matplotlib",
                 )
             except IndexError:
                 logger.error("Could not determine all peaks!")
diff --git a/src/sed/diagnostics.py b/src/sed/diagnostics.py
index 02bcc0a0..25fddd9a 100644
--- a/src/sed/diagnostics.py
+++ b/src/sed/diagnostics.py
@@ -88,7 +88,7 @@ def grid_histogram(
     if legkwds is None:
         legkwds = {}
 
-    figsz = kwds.pop("figsize", (14, 8))
+    figsz = kwds.pop("figsize", (10, 7))
 
     if len(kwds) > 0:
         raise TypeError(f"grid_histogram() got unexpected keyword arguments {kwds.keys()}.")

From dd913139515a695a1e461290a6236613e8946d57 Mon Sep 17 00:00:00 2001
From: rettigl <l.rettig@web.de>
Date: Tue, 15 Oct 2024 21:44:43 +0200
Subject: [PATCH 2/7] change color map to default plt cycle

---
 src/sed/calibrator/energy.py | 9 ++++++---
 src/sed/core/processor.py    | 3 +++
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/sed/calibrator/energy.py b/src/sed/calibrator/energy.py
index 7f1426f9..b5d055dd 100644
--- a/src/sed/calibrator/energy.py
+++ b/src/sed/calibrator/energy.py
@@ -355,7 +355,7 @@ def adjust_ranges(
         plot_segs = []
         plot_peaks = []
         fig, ax = plt.subplots(figsize=figsize)
-        colors = plt.get_cmap("rainbow")(np.linspace(0, 1, len(traces)))
+        colors = it.cycle(plt.rcParams["axes.prop_cycle"].by_key()["color"])
         for itr, color in zip(range(len(traces)), colors):
             trace = traces[itr, :]
             # main traces
@@ -378,6 +378,9 @@ def adjust_ranges(
             plot_peaks.append(scatt)
         ax.legend(fontsize=8, loc="upper right")
         ax.set_title("")
+        plt.xlabel("Time-of-flight")
+        plt.ylabel("Intensity")
+        plt.tight_layout()
 
         def update(refid, ranges):
             self.add_ranges(ranges, refid, traces=traces, **kwds)
@@ -667,8 +670,8 @@ def view(
         figsize = kwds.pop("figsize", (6, 4))
 
         if backend == "matplotlib":
-            colors = plt.get_cmap("rainbow")(np.linspace(0, 1, len(traces)))
-            fig_plt, ax = plt.subplots(figsize=figsize)
+            colors = it.cycle(plt.rcParams["axes.prop_cycle"].by_key()["color"])
+            _, ax = plt.subplots(figsize=figsize)
             for itr, color in zip(range(len(traces)), colors):
                 trace = traces[itr, :]
                 if align:
diff --git a/src/sed/core/processor.py b/src/sed/core/processor.py
index b23dfa74..6c51acfb 100644
--- a/src/sed/core/processor.py
+++ b/src/sed/core/processor.py
@@ -1245,6 +1245,9 @@ def load_bias_series(
             xaxis=self.ec.tof,
             backend="matplotlib",
         )
+        plt.xlabel("Time-of-flight")
+        plt.ylabel("Intensity")
+        plt.tight_layout()
 
     # 2. extract ranges and get peak positions
     @call_logger(logger)

From 6f5f0333a435e79bc7b1ee814c1a28a7bdf59857 Mon Sep 17 00:00:00 2001
From: rettigl <l.rettig@web.de>
Date: Tue, 15 Oct 2024 22:54:43 +0200
Subject: [PATCH 3/7] use matplotlib also for momentum correction

---
 .cspell/custom-dictionary.txt  |  2 ++
 src/sed/calibrator/momentum.py | 22 ++++++++++++++--------
 src/sed/core/processor.py      | 20 ++++++++++++--------
 src/sed/diagnostics.py         | 23 +++++++++++++----------
 4 files changed, 41 insertions(+), 26 deletions(-)

diff --git a/.cspell/custom-dictionary.txt b/.cspell/custom-dictionary.txt
index 38f8c89c..88ff0b12 100644
--- a/.cspell/custom-dictionary.txt
+++ b/.cspell/custom-dictionary.txt
@@ -404,6 +404,7 @@ xpos
 xratio
 xrng
 xscale
+xticks
 xtrans
 Xuser
 xval
@@ -414,6 +415,7 @@ ylabel
 ypos
 yratio
 yscale
+yticks
 ytrans
 zain
 Zenodo
diff --git a/src/sed/calibrator/momentum.py b/src/sed/calibrator/momentum.py
index 36a41b86..534ad81f 100644
--- a/src/sed/calibrator/momentum.py
+++ b/src/sed/calibrator/momentum.py
@@ -1348,7 +1348,9 @@ def view(
 
         if annotated:
             tsr, tsc = kwds.pop("textshift", (3, 3))
-            txtsize = kwds.pop("textsize", 12)
+            txtsize = kwds.pop("textsize", 10)
+
+        title = kwds.pop("title", "")
 
         # Handle unexpected kwds:
         handled_kwds = {"figsize"}
@@ -1358,7 +1360,7 @@ def view(
             )
 
         if backend == "matplotlib":
-            fig_plt, ax = plt.subplots(figsize=figsize)
+            _, ax = plt.subplots(figsize=figsize)
             ax.imshow(image.T, origin=origin, cmap=cmap, **imkwds)
 
             if cross:
@@ -1368,15 +1370,12 @@ def view(
 
             # Add annotation to the figure
             if annotated:
-                for (
-                    p_keys,  # pylint: disable=unused-variable
-                    p_vals,
-                ) in points.items():
+                for p_keys, p_vals in points.items():
                     try:
-                        ax.scatter(p_vals[:, 0], p_vals[:, 1], **scatterkwds)
+                        ax.scatter(p_vals[:, 0], p_vals[:, 1], s=15, **scatterkwds)
                     except IndexError:
                         try:
-                            ax.scatter(p_vals[0], p_vals[1], **scatterkwds)
+                            ax.scatter(p_vals[0], p_vals[1], s=15, **scatterkwds)
                         except IndexError:
                             pass
 
@@ -1389,6 +1388,13 @@ def view(
                                 fontsize=txtsize,
                             )
 
+            if crosshair and self.pcent is not None:
+                for radius in crosshair_radii:
+                    circle = plt.Circle(self.pcent, radius, color="k", fill=False)
+                    ax.add_patch(circle)
+
+            ax.set_title(title)
+
         elif backend == "bokeh":
             output_notebook(hide_banner=True)
             colors = it.cycle(ColorCycle[10])
diff --git a/src/sed/core/processor.py b/src/sed/core/processor.py
index 6c51acfb..5888855d 100644
--- a/src/sed/core/processor.py
+++ b/src/sed/core/processor.py
@@ -649,24 +649,28 @@ def generate_splinewarp(
         self.mc.spline_warp_estimate(use_center=use_center, **kwds)
 
         if self.mc.slice is not None and self._verbose:
-            print("Original slice with reference features")
-            self.mc.view(annotated=True, backend="bokeh", crosshair=True)
+            self.mc.view(
+                annotated=True,
+                backend="matplotlib",
+                crosshair=True,
+                title="Original slice with reference features",
+            )
 
-            print("Corrected slice with target features")
             self.mc.view(
                 image=self.mc.slice_corrected,
                 annotated=True,
                 points={"feats": self.mc.ptargs},
-                backend="bokeh",
+                backend="matplotlib",
                 crosshair=True,
+                title="Corrected slice with target features",
             )
 
-            print("Original slice with target features")
             self.mc.view(
                 image=self.mc.slice,
                 points={"feats": self.mc.ptargs},
                 annotated=True,
-                backend="bokeh",
+                backend="matplotlib",
+                title="Original slice with target features",
             )
 
     # 3a. Save spline-warp parameters to config file.
@@ -2384,7 +2388,7 @@ def view_event_histogram(
         bins: Sequence[int] = None,
         axes: Sequence[str] = None,
         ranges: Sequence[tuple[float, float]] = None,
-        backend: str = "bokeh",
+        backend: str = "matplotlib",
         legend: bool = True,
         histkwds: dict = None,
         legkwds: dict = None,
@@ -2403,7 +2407,7 @@ def view_event_histogram(
             ranges (Sequence[tuple[float, float]], optional): Value ranges of all
                 specified axes. Defaults to config["histogram"]["ranges"].
             backend (str, optional): Backend of the plotting library
-                ('matplotlib' or 'bokeh'). Defaults to "bokeh".
+                ("matplotlib" or "bokeh"). Defaults to "matplotlib".
             legend (bool, optional): Option to include a legend in the histogram plots.
                 Defaults to True.
             histkwds (dict, optional): Keyword arguments for histograms
diff --git a/src/sed/diagnostics.py b/src/sed/diagnostics.py
index 25fddd9a..6ec8e507 100644
--- a/src/sed/diagnostics.py
+++ b/src/sed/diagnostics.py
@@ -59,7 +59,7 @@ def grid_histogram(
     rvs: Sequence,
     rvbins: Sequence,
     rvranges: Sequence[tuple[float, float]],
-    backend: str = "bokeh",
+    backend: str = "matplotlib",
     legend: bool = True,
     histkwds: dict = None,
     legkwds: dict = None,
@@ -73,22 +73,22 @@ def grid_histogram(
         rvs (Sequence): List of names for the random variables (rvs).
         rvbins (Sequence): Bin values for all random variables.
         rvranges (Sequence[tuple[float, float]]): Value ranges of all random variables.
-        backend (str, optional): Backend for making the plot ('matplotlib' or 'bokeh').
-            Defaults to "bokeh".
+        backend (str, optional): Backend for making the plot ("matplotlib" or "bokeh").
+            Defaults to "matplotlib".
         legend (bool, optional): Option to include a legend in each histogram plot.
             Defaults to True.
         histkwds (dict, optional): Keyword arguments for histogram plots.
             Defaults to None.
         legkwds (dict, optional): Keyword arguments for legends. Defaults to None.
         **kwds:
-            - *figsize*: Figure size. Defaults to (14, 8)
+            - *figsize*: Figure size. Defaults to (6, 4)
     """
     if histkwds is None:
         histkwds = {}
     if legkwds is None:
         legkwds = {}
 
-    figsz = kwds.pop("figsize", (10, 7))
+    figsz = kwds.pop("figsize", (6, 4))
 
     if len(kwds) > 0:
         raise TypeError(f"grid_histogram() got unexpected keyword arguments {kwds.keys()}.")
@@ -96,7 +96,7 @@ def grid_histogram(
     if backend == "matplotlib":
         nrv = len(rvs)
         nrow = int(np.ceil(nrv / ncol))
-        histtype = kwds.pop("histtype", "step")
+        histtype = kwds.pop("histtype", "bar")
 
         fig, ax = plt.subplots(nrow, ncol, figsize=figsz)
         otherax = ax.copy()
@@ -114,7 +114,7 @@ def grid_histogram(
                     **histkwds,
                 )
                 if legend:
-                    ax[axind].legend(fontsize=15, **legkwds)
+                    ax[axind].legend(fontsize=10, **legkwds)
 
                 otherax[axind] = None
 
@@ -128,13 +128,16 @@ def grid_histogram(
                     **histkwds,
                 )
                 if legend:
-                    ax[i].legend(fontsize=15, **legkwds)
+                    ax[i].legend(fontsize=10, **legkwds)
 
                 otherax[i] = None
 
         for oax in otherax.flatten():
             if oax is not None:
                 fig.delaxes(oax)
+        plt.xticks(fontsize=8)
+        plt.yticks(fontsize=8)
+        plt.tight_layout()
 
     elif backend == "bokeh":
         output_notebook(hide_banner=True)
@@ -163,7 +166,7 @@ def grid_histogram(
             gridplot(
                 plots,  # type: ignore
                 ncols=ncol,
-                width=figsz[0] * 30,
-                height=figsz[1] * 28,
+                width=figsz[0] * 100 // ncol,
+                height=figsz[1] * 100 // (len(plots) // ncol),
             ),
         )

From 366de39badeb9bae4413acec8eff344e78f3c7b8 Mon Sep 17 00:00:00 2001
From: rettigl <l.rettig@web.de>
Date: Tue, 15 Oct 2024 22:59:17 +0200
Subject: [PATCH 4/7] fix type error

---
 src/sed/calibrator/momentum.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sed/calibrator/momentum.py b/src/sed/calibrator/momentum.py
index 534ad81f..75b7425f 100644
--- a/src/sed/calibrator/momentum.py
+++ b/src/sed/calibrator/momentum.py
@@ -102,7 +102,7 @@ def __init__(
         self.include_center: bool = False
         self.use_center: bool = False
         self.pouter: np.ndarray = None
-        self.pcent: tuple[float, ...] = None
+        self.pcent: tuple[float, float] = None
         self.pouter_ord: np.ndarray = None
         self.prefs: np.ndarray = None
         self.ptargs: np.ndarray = None

From 6365b930166c2f083a0c4fd8854ff5ace680936f Mon Sep 17 00:00:00 2001
From: rettigl <l.rettig@web.de>
Date: Wed, 16 Oct 2024 13:26:24 +0200
Subject: [PATCH 5/7] fix figure sizes and font sizes

---
 .cspell/custom-dictionary.txt |  3 +++
 src/sed/diagnostics.py        | 16 ++++++++++------
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/.cspell/custom-dictionary.txt b/.cspell/custom-dictionary.txt
index 88ff0b12..546e29ae 100644
--- a/.cspell/custom-dictionary.txt
+++ b/.cspell/custom-dictionary.txt
@@ -334,6 +334,7 @@ scicat
 SDIAG
 sdir
 segs
+setp
 sfile
 shutil
 Sixten
@@ -404,6 +405,7 @@ xpos
 xratio
 xrng
 xscale
+xticklabels
 xticks
 xtrans
 Xuser
@@ -415,6 +417,7 @@ ylabel
 ypos
 yratio
 yscale
+yticklabels
 yticks
 ytrans
 zain
diff --git a/src/sed/diagnostics.py b/src/sed/diagnostics.py
index 6ec8e507..4f44b1f7 100644
--- a/src/sed/diagnostics.py
+++ b/src/sed/diagnostics.py
@@ -88,7 +88,7 @@ def grid_histogram(
     if legkwds is None:
         legkwds = {}
 
-    figsz = kwds.pop("figsize", (6, 4))
+    figsz = kwds.pop("figsize", (3, 2))  # figure size of each panel
 
     if len(kwds) > 0:
         raise TypeError(f"grid_histogram() got unexpected keyword arguments {kwds.keys()}.")
@@ -98,13 +98,16 @@ def grid_histogram(
         nrow = int(np.ceil(nrv / ncol))
         histtype = kwds.pop("histtype", "bar")
 
-        fig, ax = plt.subplots(nrow, ncol, figsize=figsz)
+        figsize = [figsz[0] * ncol, figsz[1] * nrow]
+        fig, ax = plt.subplots(nrow, ncol, figsize=figsize)
         otherax = ax.copy()
         for i, zipped in enumerate(zip(rvs, rvbins, rvranges)):
             # Make each histogram plot
             rvname, rvbin, rvrg = zipped
             try:
                 axind = np.unravel_index(i, (nrow, ncol))
+                plt.setp(ax[axind].get_xticklabels(), fontsize=8)
+                plt.setp(ax[axind].get_yticklabels(), fontsize=8)
                 ax[axind].hist(
                     dct[rvname],
                     bins=rvbin,
@@ -119,6 +122,8 @@ def grid_histogram(
                 otherax[axind] = None
 
             except IndexError:
+                plt.setp(ax[i].get_xticklabels(), fontsize=8)
+                plt.setp(ax[i].get_yticklabels(), fontsize=8)
                 ax[i].hist(
                     dct[rvname],
                     bins=rvbin,
@@ -135,8 +140,7 @@ def grid_histogram(
         for oax in otherax.flatten():
             if oax is not None:
                 fig.delaxes(oax)
-        plt.xticks(fontsize=8)
-        plt.yticks(fontsize=8)
+
         plt.tight_layout()
 
     elif backend == "bokeh":
@@ -166,7 +170,7 @@ def grid_histogram(
             gridplot(
                 plots,  # type: ignore
                 ncols=ncol,
-                width=figsz[0] * 100 // ncol,
-                height=figsz[1] * 100 // (len(plots) // ncol),
+                width=figsz[0] * 100,
+                height=figsz[1] * 100,
             ),
         )

From fb0b025a0d653387d0748dc1b9e0326c27677492 Mon Sep 17 00:00:00 2001
From: rettigl <l.rettig@web.de>
Date: Wed, 13 Nov 2024 09:11:28 +0100
Subject: [PATCH 6/7] remove redundant toctree entry

---
 docs/user_guide/advanced_topics.md | 6 ------
 docs/user_guide/index.md           | 5 +++--
 2 files changed, 3 insertions(+), 8 deletions(-)
 delete mode 100644 docs/user_guide/advanced_topics.md

diff --git a/docs/user_guide/advanced_topics.md b/docs/user_guide/advanced_topics.md
deleted file mode 100644
index ebd773c8..00000000
--- a/docs/user_guide/advanced_topics.md
+++ /dev/null
@@ -1,6 +0,0 @@
-```{toctree}
-:maxdepth: 1
-../tutorial/6_binning_with_time-stamped_data
-../tutorial/7_correcting_orthorhombic_symmetry
-../tutorial/8_jittering_tutorial
-```
diff --git a/docs/user_guide/index.md b/docs/user_guide/index.md
index 16d36aaf..12485b87 100644
--- a/docs/user_guide/index.md
+++ b/docs/user_guide/index.md
@@ -22,8 +22,9 @@ config
 ```
 
 ## Advanced Topics
-
 ```{toctree}
 :maxdepth: 1
-advanced_topics
+../tutorial/6_binning_with_time-stamped_data
+../tutorial/7_correcting_orthorhombic_symmetry
+../tutorial/8_jittering_tutorial
 ```

From 7ff8fc2a7a1ee4f9873035085f6cdb00b2f50077 Mon Sep 17 00:00:00 2001
From: rettigl <l.rettig@web.de>
Date: Wed, 13 Nov 2024 09:40:04 +0100
Subject: [PATCH 7/7] fix config docs

---
 docs/user_guide/config.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/user_guide/config.md b/docs/user_guide/config.md
index 7fb62f7d..450d4da2 100644
--- a/docs/user_guide/config.md
+++ b/docs/user_guide/config.md
@@ -12,18 +12,18 @@ The config mechanism returns the combined dictionary, and reports the loaded con
 
 ## Default configuration settings
 
-```{literalinclude} ../../sed/config/default.yaml
+```{literalinclude} ../../config/default.yaml
 :language: yaml
 ```
 
 ## Example configuration file for mpes (METIS momentum microscope at FHI-Berlin)
 
-```{literalinclude} ../../sed/config/mpes_example_config.yaml
+```{literalinclude} ../../config/mpes_example_config.yaml
 :language: yaml
 ```
 
 ## Example configuration file for flash (HEXTOF momentum microscope at FLASH, Desy)
 
-```{literalinclude} ../../sed/config/flash_example_config.yaml
+```{literalinclude} ../../config/flash_example_config.yaml
 :language: yaml
 ```