allow darkmode and update plotting the lixel summation

plenoirf/summary/figure.py

@@ -1,4 +1,5 @@
 import numpy as np
+from plenopy.light_field_geometry.LightFieldGeometry import init_lixel_polygons
 
 
 FIGURE_STYLE = {"rows": 720, "cols": 1280, "fontsize": 1.0}
@@ -113,15 +114,12 @@ def is_in_roi(x, y, roi, margin=0.1):
         return False
 
 
-def position_of_eye(light_field_geometry, eye_id):
+def position_of_eye(light_field_geometry, lixel_polygons, eye_id):
+    poly = lixel_polygons
     num_pax = light_field_geometry.number_paxel
     start = eye_id * num_pax
     stop = (eye_id + 1) * num_pax
-    poly = plenopy.light_field_geometry.init_lixel_polygons(
-        lixel_positions_x=light_field_geometry.lixel_positions_x,
-        lixel_positions_y=light_field_geometry.lixel_positions_y,
-        lixel_outer_radius=light_field_geometry.lixel_outer_radius,
-    )
+
     poly = poly[start:stop]
     poly = np.array(poly)
     pp = []
@@ -135,11 +133,15 @@ def position_of_eye(light_field_geometry, eye_id):
     return np.array([x_mean, y_mean])
 
 
-def positions_of_eyes_in_roi(light_field_geometry, roi, margin=0.1):
+def positions_of_eyes_in_roi(
+    light_field_geometry, lixel_polygons, roi, margin=0.1
+):
     positions_of_eyes = {}
     for eye_id in range(light_field_geometry.number_pixel):
         pos = position_of_eye(
-            light_field_geometry=light_field_geometry, eye_id=eye_id
+            light_field_geometry=light_field_geometry,
+            lixel_polygons=lixel_polygons,
+            eye_id=eye_id,
         )
         if is_in_roi(x=pos[0], y=pos[1], roi=roi, margin=margin):
             positions_of_eyes[eye_id] = pos

plenoirf/summary/scripts/0212_trajectory_debugging_with_example_events.py

@@ -137,8 +137,10 @@ def read_shower_maximum_object_distance(
         structure=irf.table.STRUCTURE,
     )
 
-    return irf.production.estimate_primary_trajectory.get_column_as_dict_by_index(
-        table=event_table, level_key="features", column_key=key
+    return (
+        irf.production.estimate_primary_trajectory.get_column_as_dict_by_index(
+            table=event_table, level_key="features", column_key=key
+        )
     )
 
 

plenoirf/summary/scripts/1100_plot_summation_lixels_into_seven_pixels.py

@@ -5,28 +5,53 @@
 import os
 import numpy as np
 import json_utils
+import json
 import sebastians_matplotlib_addons as seb
 import matplotlib
 from matplotlib.collections import PolyCollection
+from plenopy.light_field_geometry.LightFieldGeometry import init_lixel_polygons
 
-argv = irf.summary.argv_since_py(sys.argv)
-pa = irf.summary.paths_from_argv(argv)
-
-sum_config = irf.summary.read_summary_config(summary_dir=paths["analysis_dir"])
-seb.matplotlib.rcParams.update(sum_config["plot"]["matplotlib"])
+DARKMODE = True
+rrr = 2
 
+paths = irf.summary.paths_from_argv(sys.argv)
+res = irf.summary.Resources.from_argv(sys.argv)
 os.makedirs(paths["out_dir"], exist_ok=True)
 
+if DARKMODE:
+    seb.plt.style.use("dark_background")
+    stroke = "white"
+    backc = "black"
+    EXT = ".dark.png"
+    cmap = "binary_r"
+    BEAM_ALPHA = 0.4
+    colors = ["gray", "g", "b", "r", "c", "m", "orange"]
+else:
+    EXT = ".jpg"
+    stroke = "black"
+    backc = "white"
+    cmap = "binary"
+    BEAM_ALPHA = 0.2
+    colors = ["k", "g", "b", "r", "c", "m", "orange"]
+
+seb.matplotlib.rcParams.update(res.analysis["plot"]["matplotlib"])
+
 light_field_geometry = pl.LightFieldGeometry(
-    os.path.join(paths["plenoirf_dir"], "light_field_geometry")
+    os.path.join(
+        paths["plenoirf_dir"],
+        "plenoptics",
+        "instruments",
+        res.instrument_key,
+        "light_field_geometry",
+    )
 )
 
 region_of_interest_on_sensor_plane = {"x": [-0.35, 0.35], "y": [-0.35, 0.35]}
 
 object_distances = [21e3, 29e3, 999e3]
 # object_distances = [3e3, 5e3, 9e3, 15e3, 25e3, 999e3]
 central_seven_pixel_ids = [4221, 4124, 4222, 4220, 4125, 4317, 4318]
-colors = ["k", "g", "b", "r", "c", "m", "orange"]
+
 
 XY_LABELS_ALWAYS = True
 
@@ -56,30 +81,33 @@
 def lixel_in_region_of_interest(
     light_field_geometry, lixel_id, roi, margin=0.1
 ):
-    return is_in_roi(
+    return irf.summary.figure.is_in_roi(
         x=light_field_geometry.lixel_positions_x[lixel_id],
         y=light_field_geometry.lixel_positions_y[lixel_id],
         roi=roi,
         margin=margin,
     )
 
 
+lixel_polygons = init_lixel_polygons(
+    lixel_positions_x=light_field_geometry.lixel_positions_x,
+    lixel_positions_y=light_field_geometry.lixel_positions_y,
+    lixel_outer_radius=light_field_geometry.lixel_outer_radius,
+)
+
 poseye = irf.summary.figure.positions_of_eyes_in_roi(
     light_field_geometry=light_field_geometry,
+    lixel_polygons=lixel_polygons,
     roi=region_of_interest_on_sensor_plane,
     margin=0.2,
 )
 
 AXES_STYLE = {"spines": ["left", "bottom"], "axes": ["x", "y"], "grid": False}
 
-lixel_polygons = pl.light_field_geometry.init_lixel_polygons(
-    lixel_positions_x=light_field_geometry.lixel_positions_x,
-    lixel_positions_y=light_field_geometry.lixel_positions_y,
-    lixel_outer_radius=light_field_geometry.lixel_outer_radius,
-)
-
 for obj, object_distance in enumerate(object_distances):
-    fig = seb.figure(style={"rows": 960, "cols": 1280, "fontsize": 1.244})
+    fig = seb.figure(
+        style={"rows": 960 * rrr, "cols": 1280 * rrr, "fontsize": 1.244 * rrr}
+    )
     ax = seb.add_axes(
         fig=fig, span=[0.15, 0.15, 0.85 * (3 / 4), 0.85], style=AXES_STYLE
     )
@@ -104,9 +132,10 @@ def lixel_in_region_of_interest(
             )
         )
 
-        json_utils.write(path=cpath, out_dict=lixel_to_pixel, indent=None)
+        json_utils.write(cpath, lixel_to_pixel, indent=None)
     else:
-        lixel_to_pixel = json_utils.read(path=cpath)
+        with open(cpath, "rt") as f:
+            lixel_to_pixel = json.loads(f.read())
 
     colored_lixels = np.zeros(light_field_geometry.number_lixel, dtype=bool)
     for i, pixel_id in enumerate(central_seven_pixel_ids):
@@ -143,7 +172,7 @@ def lixel_in_region_of_interest(
 
     coll = PolyCollection(
         not_colored_polygons,
-        facecolors=["w" for _ in range(len(not_colored_polygons))],
+        facecolors=[backc for _ in range(len(not_colored_polygons))],
         edgecolors="gray",
         linewidths=linewidths,
     )
@@ -157,7 +186,7 @@ def lixel_in_region_of_interest(
             y=_y,
             r_outer=eye_outer_radius_m,
             orientation_deg=0,
-            color="black",
+            color=stroke,
             linestyle="-",
             linewidth=linewidths * 2,
         )
@@ -179,15 +208,15 @@ def lixel_in_region_of_interest(
         N=9,
         linewidth=4.7,
         color=irf.summary.figure.COLOR_BEAM_RGBA,
-        alpha=0.2,
+        alpha=BEAM_ALPHA,
     )
     ax2.plot(
         [
             -1,
             1,
         ],
         [-0.1, -0.1],
-        color="white",
+        color=backc,
         linewidth=10,
         alpha=1.0,
     )
@@ -197,7 +226,7 @@ def lixel_in_region_of_interest(
             1.0,
         ],
         [0, 0],
-        color="k",
+        color=stroke,
         linewidth=0.5 * linewidths,
     )
 
@@ -213,7 +242,9 @@ def lixel_in_region_of_interest(
     fig.savefig(
         os.path.join(
             paths["out_dir"],
-            "refocus_lixel_summation_7_{obj:d}.jpg".format(obj=obj),
+            "refocus_lixel_summation_7_{obj:d}{ext:s}".format(
+                obj=obj, ext=EXT
+            ),
         )
     )
     seb.close("all")

plenoirf/summary/scripts/1110_plot_summation_photo_sensors_into_pixels_to_compensate_aberrations.py

@@ -7,19 +7,39 @@
 import json_utils
 import numpy as np
 import sebastians_matplotlib_addons as seb
+from plenopy.light_field_geometry.LightFieldGeometry import init_lixel_polygons
 
-argv = irf.summary.argv_since_py(sys.argv)
-pa = irf.summary.paths_from_argv(argv)
+DARKMODE = False
+rrr = 1
 
-sum_config = irf.summary.read_summary_config(summary_dir=paths["analysis_dir"])
-seb.matplotlib.rcParams.update(sum_config["plot"]["matplotlib"])
+paths = irf.summary.paths_from_argv(sys.argv)
+res = irf.summary.Resources.from_argv(sys.argv)
+os.makedirs(paths["out_dir"], exist_ok=True)
+
+if DARKMODE:
+    seb.plt.style.use("dark_background")
+    stroke = "white"
+    EXT = ".dark.png"
+    cmap = "binary_r"
+else:
+    EXT = ".jpg"
+    stroke = "black"
+    cmap = "binary"
+
+seb.matplotlib.rcParams.update(res.analysis["plot"]["matplotlib"])
 
 AXES_STYLE = {"spines": ["left", "bottom"], "axes": ["x", "y"], "grid": False}
 
 os.makedirs(paths["out_dir"], exist_ok=True)
 
 light_field_geometry = pl.LightFieldGeometry(
-    os.path.join(paths["plenoirf_dir"], "light_field_geometry")
+    os.path.join(
+        paths["plenoirf_dir"],
+        "plenoptics",
+        "instruments",
+        res.instrument_key,
+        "light_field_geometry",
+    )
 )
 
 OBJECT_DISTANCE = 999e3
@@ -86,14 +106,16 @@
 
 ROI_RADIUS = 0.35
 
-lixel_polygons = pl.light_field_geometry.init_lixel_polygons(
+lixel_polygons = init_lixel_polygons(
     lixel_positions_x=light_field_geometry.lixel_positions_x,
     lixel_positions_y=light_field_geometry.lixel_positions_y,
     lixel_outer_radius=light_field_geometry.lixel_outer_radius,
 )
 
 for pixel in pixels:
-    fig = seb.figure(style={"rows": 360, "cols": 360, "fontsize": 0.7})
+    fig = seb.figure(
+        style={"rows": 360 * rrr, "cols": 360 * rrr, "fontsize": 0.7 * rrr}
+    )
     ax = seb.add_axes(fig=fig, span=[0.0, 0.0, 1, 1], style=AXES_STYLE)
 
     _x, _y = pixel["mean_position_of_photosensors_on_sensor_plane"]
@@ -102,6 +124,7 @@
 
     poseye = irf.summary.figure.positions_of_eyes_in_roi(
         light_field_geometry=light_field_geometry,
+        lixel_polygons=lixel_polygons,
         roi={"x": xlim, "y": ylim},
         margin=0.2,
     )
@@ -110,7 +133,7 @@
         polygons=lixel_polygons,
         I=pixel["photosensor_mask"],
         ax=ax,
-        cmap="binary",
+        cmap=cmap,
         edgecolors="grey",
         linewidths=0.33,
         xlim=xlim,
@@ -125,7 +148,7 @@
             y=_y,
             r_outer=eye_outer_radius_m,
             orientation_deg=0,
-            color="black",
+            color=stroke,
             linestyle="-",
             linewidth=0.5,
         )
@@ -145,16 +168,18 @@
     fig.savefig(
         os.path.join(
             paths["out_dir"],
-            "aberration_pixel_{pixel:0d}_{angle:0d}mdeg.jpg".format(
-                pixel=pixel["id"], angle=off_axis_angle_mdeg
+            "aberration_pixel_{pixel:0d}_{angle:0d}mdeg{ext:s}".format(
+                pixel=pixel["id"], angle=off_axis_angle_mdeg, ext=EXT
             ),
         ),
     )
     seb.close("all")
 
 # plot all pixels overview
 # -------------------------
-fig = fig = seb.figure(style={"rows": 720, "cols": 720, "fontsize": 0.7})
+fig = fig = seb.figure(
+    style={"rows": 720 * rrr, "cols": 720 * rrr, "fontsize": 0.7 * rrr}
+)
 ax = seb.add_axes(fig=fig, span=[0.16, 0.16, 0.82, 0.82])
 
 overview_photosensor_mask = np.zeros(
@@ -167,13 +192,14 @@
     polygons=lixel_polygons,
     I=overview_photosensor_mask,
     ax=ax,
-    cmap="binary",
+    cmap=cmap,
     edgecolors="grey",
     linewidths=(0.02,),
 )
 
 poseye = irf.summary.figure.positions_of_eyes_in_roi(
     light_field_geometry=light_field_geometry,
+    lixel_polygons=lixel_polygons,
     roi={"x": [-10, 10], "y": [-10, 10]},
     margin=0.2,
 )
@@ -186,7 +212,7 @@
         y=_y,
         r_outer=eye_outer_radius_m,
         orientation_deg=0,
-        color="black",
+        color=stroke,
         linestyle="-",
         alpha=0.5,
         linewidth=0.2,
@@ -222,7 +248,7 @@
 ax.set_xlabel("$x\\,/\\,$m")
 ax.set_ylabel("$y\\,/\\,$m")
 
-fig.savefig(os.path.join(paths["out_dir"], "aberration_overview.jpg"))
+fig.savefig(os.path.join(paths["out_dir"], "aberration_overview" + EXT))
 seb.close("all")
 
 # export table