From 2e89af5996442dfd3ddecc716168b37638874b4e Mon Sep 17 00:00:00 2001
From: David Hammer <david.hammer@xfel.eu>
Date: Wed, 23 Jun 2021 09:48:33 +0200
Subject: [PATCH] Dropping legacy_colorbar to avoid warning, fixing label color
bug, making bad pixel plot binary
---
src/cal_tools/plotting.py | 63 +++++++++++++++++++++++++--------------
1 file changed, 41 insertions(+), 22 deletions(-)
diff --git a/src/cal_tools/plotting.py b/src/cal_tools/plotting.py
index 8c43424ef..d2434ffaf 100644
--- a/src/cal_tools/plotting.py
+++ b/src/cal_tools/plotting.py
@@ -14,8 +14,12 @@ from matplotlib import colors
from matplotlib.patches import Patch
from mpl_toolkits.axes_grid1 import AxesGrid
+plt.rcParams["mpl_toolkits.legacy_colorbar"] = False
-def show_overview(d, cell_to_preview, gain_to_preview, out_folder=None, infix=None):
+
+def show_overview(
+ d, cell_to_preview, gain_to_preview, out_folder=None, infix=None
+):
"""
Show an overview
:param d: A dict with the number of modules and
@@ -40,8 +44,9 @@ def show_overview(d, cell_to_preview, gain_to_preview, out_folder=None, infix=No
cbar_size="7%",
cbar_pad="2%",
)
- i = 0
- for key, item in data.items():
+
+ items = list(data.items())
+ for ax, cbar_ax, (key, item) in zip(grid, grid.cbar_axes, items):
cf = 0
if "ThresholdsDark" in key:
cf = -1
@@ -60,11 +65,14 @@ def show_overview(d, cell_to_preview, gain_to_preview, out_folder=None, infix=No
item[..., cell_to_preview, gain_to_preview + cf].size > 0.01): # noqa
bound *= 2
- if "BadPixelsDark" in key:
- im = grid[i].imshow(np.log2(item[..., cell_to_preview,
- gain_to_preview + cf]),
- interpolation="nearest", vmin=0, vmax=8,
- aspect='auto')
+ is_badpixels = "BadPixels" in key
+
+ if is_badpixels:
+ im = ax.imshow(
+ item[..., cell_to_preview, gain_to_preview + cf] != 0,
+ cmap=plt.cm.colors.ListedColormap(["w", "k"]),
+ aspect="auto",
+ )
else:
if len(item.shape) == 4:
@@ -78,27 +86,33 @@ def show_overview(d, cell_to_preview, gain_to_preview, out_folder=None, infix=No
im_prev = np.moveaxis(item[..., cell_to_preview], 0, 1)
vmax = med + np.abs(bound * medscale)
- im = grid[i].imshow(im_prev, interpolation="nearest",
- vmin=med - np.abs(bound * medscale),
- vmax=vmax, aspect='auto')
+ im = ax.imshow(im_prev, interpolation="nearest",
+ vmin=med - np.abs(bound * medscale),
+ vmax=vmax, aspect='auto')
+
+ cb = cbar_ax.colorbar(im)
+ if is_badpixels:
+ cb.set_ticks([0.25, 0.75])
+ cb.set_ticklabels(["good", "bad"])
+ else:
+ cb.set_label("ADU")
- cb = grid.cbar_axes[i].colorbar(im)
- cb.set_label_text("ADU" if key != "BadPixels" else "Bad Pixel Code")
+ ax.text(
+ 5, 20, key, color="k" if is_badpixels else "w", fontsize=20
+ )
- grid[i].text(5, 20, key, color="w" if key != "BadPixels" else "k", fontsize=20) # noqa
+ grid[0].text(5, 50, module, color="k" if "BadPixels" in items[0][0] else "r", fontsize=20) # noqa
- i += 1
- grid[0].text(5, 50, module, color="r" if key != "BadPixels" else "k", fontsize=20) # noqa
if out_folder and infix:
fig.savefig(f"{out_folder}/"
f"dark_analysis_{infix}_module_{module}.png")
def rebin(a, *args):
- '''rebin ndarray data into a smaller ndarray of the same rank whose dimensions
- are factors of the original dimensions. eg. An array with 6 columns and 4 rows
- can be reduced to have 6,3,2 or 1 columns and 4,2 or 1 rows.
- example usages:
+ '''rebin ndarray data into a smaller ndarray of the same rank whose
+ dimensions are factors of the original dimensions. eg. An array with 6
+ columns and 4 rows can be reduced to have 6,3,2 or 1 columns and 4,2 or 1
+ rows. example usages:
https://scipy-cookbook.readthedocs.io/items/Rebinning.html
>>> a=rand(6,4); b=rebin(a,3,2)
>>> a=rand(6); b=rebin(a,2)
@@ -116,7 +130,12 @@ def rebin(a, *args):
def plot_badpix_3d(data, definitions, title=None, rebin_fac=2, azim=22.5):
od = data
- d, dims = rebin(od.astype(np.uint32), od.shape[0] // rebin_fac, od.shape[1] // rebin_fac, od.shape[2])
+ d, dims = rebin(
+ od.astype(np.uint32),
+ od.shape[0] // rebin_fac,
+ od.shape[1] // rebin_fac,
+ od.shape[2],
+ )
xx, yy, zz = dims
voxels = d.astype(np.bool)
colors = np.full(voxels.shape, '#FFFFFF')
@@ -137,7 +156,7 @@ def plot_badpix_3d(data, definitions, title=None, rebin_fac=2, azim=22.5):
ax.set_zlim(0, np.max(zz))
for k, c in cols.items():
- ax.plot([-1,], [-1,], color=c[1], label=c[0])
+ ax.plot([-1, ], [-1, ], color=c[1], label=c[0])
ax.legend()
if title:
ax.set_title(title)
--
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