Added more minianalyses (#278)

* bug path

* fix plot

* fix plot

* fix plot

amstrax/analyses/plotting.py

@@ -222,6 +222,9 @@ def plot_area_per_channel(context, run_id, peaks, **kwargs):
     # Get the peaks
     area_per_channel = peak["area_per_channel"]
 
+    vmin = min(area_per_channel)
+    vmax = max(area_per_channel)
+
     # Plot the area per channel
     # Four quadrants for channels 1 2 3 4
     # imshow with 4 quadrants
@@ -235,7 +238,9 @@ def plot_area_per_channel(context, run_id, peaks, **kwargs):
             -top_quadrant_length,
             top_quadrant_length,
         ],
-        origin="upper",
+        origin="lower",
+        vmin=vmin,
+        vmax=vmax,
     )
     axes[1].imshow(
         area_per_channel[0].reshape(1, 1),
@@ -246,6 +251,8 @@ def plot_area_per_channel(context, run_id, peaks, **kwargs):
             -bottom_quadrant_length,
             bottom_quadrant_length,
         ],
+        vmin=vmin,
+        vmax=vmax,
     )
 
     # Write the number of the channel in every element of imshow of axes[0]
@@ -305,6 +312,22 @@ def plot_area_per_channel(context, run_id, peaks, **kwargs):
 
 @amstrax.mini_analysis(requires=("records_led",))
 def plot_led_records(context, run_id, records_led, n_records=100, **kwargs):
+    """
+    Plots the LED records for a given run ID.
+
+    Args:
+        context (unknown): Unknown.
+        run_id (int): The ID of the run to plot.
+        records_led (unknown): Unknown.
+        n_records (int, optional): The number of records to plot. Defaults to 100.
+        **kwargs: Unknown.
+
+    Raises:
+        ValueError: If the run ID is not found in the database or if the run is not an external trigger run.
+
+    Returns:
+        None
+    """
     db = amstrax.get_mongo_collection()
 
     rd = db.find_one({"number": int(run_id)})

amstrax/analyses/quick_checks.py

@@ -81,6 +81,63 @@ def std_axes():
     std_axes()
     plt.tight_layout()
 
+
+
+@amstrax.mini_analysis(requires=('peak_basics',))
+def plot_peaks_area_aft_histogram(
+        context, run_id, peaks,
+        pe_bins=np.logspace(0, 7, 120),
+        rt_bins=np.geomspace(2, 1e5, 120),
+        extra_labels=tuple(),
+        rate_range=(1e-4, 1),
+        aft_range=(0, .85),
+        figsize=(14, 5)):
+    """Plot side-by-side (area, width) histograms of the peak rate
+    and mean area fraction top.
+
+    :param pe_bins: Array of bin edges for the peak area dimension [PE]
+    :param rt_bins: array of bin edges for the rise time dimension [ns]
+    :param extra_labels: List of (area, risetime, text, color) extra labels
+    to put on the plot
+    :param rate_range: Range of rates to show [peaks/(bin*s)]
+    :param aft_range: Range of mean S1 area fraction top / bin to show
+    :param figsize: Figure size to use
+    """
+    livetime_sec = get_livetime_sec(context, run_id, peaks)
+
+    mh = Histdd(peaks,
+                dimensions=(
+                    ('area', pe_bins),
+                    ('area_fraction_top', np.linspace(0, 1, 100)),
+                    ('range_50p_area', rt_bins),
+                ))
+
+    f, axes = plt.subplots(1, 2, figsize=figsize)
+
+    def std_axes():
+        plt.gca().set_facecolor('k')
+        plt.xscale('log')
+        plt.xlabel("Area [PE]")
+        plt.ylabel("Area Fraction Top")
+        # plt.ylabel("Range 50% area [ns]")
+
+    plt.sca(axes[0])
+    (mh / livetime_sec).sum(axis=2).plot(
+        norm=LogNorm(vmin=rate_range[0], vmax=rate_range[1]),
+        colorbar_kwargs=dict(extend='both'),
+        cblabel='Peaks / (bin * s)')
+    std_axes()
+
+    plt.sca(axes[1])
+    mh.average(axis=2).plot(
+        norm=LogNorm(vmin=rt_bins[0], vmax=rt_bins[-1]),
+        colorbar_kwargs=dict(extend='max'),
+        cmap=plt.cm.jet,
+        cblabel='Range 50% area [ns]')
+
+    std_axes()
+    plt.tight_layout()
+
 @amstrax.mini_analysis(requires=['event_info'])
 def event_scatter(context, run_id, events,
                   show_single=True,

amstrax/contexts.py

@@ -14,7 +14,7 @@
     'DEFAULT_COLLECTION': 'runs_gas'
 }
 
-PROCESSED_DATA_FOLDER = 'home/xams/data/processed'
+PROCESSED_DATA_FOLDER = '/home/xams/data/xams_processed'
 
 COMMON_OPT_XAMS = dict(
     register_all=[],

amstrax/plugins/peaks/peak_basics.py

@@ -97,7 +97,7 @@ def compute(self, peaks):
         r['n_saturated_channels'] = p['n_saturated_channels']
 
         n_top = self.config["n_top_pmts"]
-        area_top = p['area_per_channel'][:, :n_top].sum(axis=1)
+        area_top = p['area_per_channel'][:, n_top:].sum(axis=1)
         # Recalculate to prevent numerical inaccuracy #442
         area_total = p['area_per_channel'].sum(axis=1)
         # Negative-area peaks get NaN AFT