diff --git a/cal_tools/cal_tools/plotting.py b/cal_tools/cal_tools/plotting.py
index 5bafa91c67fb5fd0a1c96e7a036f2adc2ec87d2a..2eda7286b05cc55c192b2ee6339bcd5de526f28d 100644
--- a/cal_tools/cal_tools/plotting.py
+++ b/cal_tools/cal_tools/plotting.py
@@ -1,7 +1,10 @@
+from typing import Any, Dict, Optional
+
+from extra_geom import AGIPD_500K2GGeometry
import matplotlib.pyplot as plt
+from matplotlib import colors
from matplotlib.patches import Patch, Rectangle
from mpl_toolkits.axes_grid1 import AxesGrid
-from mpl_toolkits.mplot3d import Axes3D
import numpy as np
@@ -92,7 +95,6 @@ def rebin(a, *args):
'''
shape = a.shape
lenShape = len(shape)
- factor = np.asarray(shape) // np.asarray(args)
evList = ['a.reshape('] + \
['args[%d],factor[%d],' % (i, i) for i in range(lenShape)] + \
[')'] + ['.sum(%d)' % (i + 1) for i in range(lenShape)] + \
@@ -199,7 +201,8 @@ def create_constant_overview(constant, name, cells, vmin=None, vmax=None,
ax.set_ylim(vmin, vmax)
-def show_processed_modules(dinstance, constants, mnames, mode):
+def show_processed_modules(dinstance: str, constants: Optional[Dict[str, Any]],
+ mnames: str, mode: str):
"""
Show the status of the processed modules.
Green: Processed. Gray: Not Processed. Red: No data available.
@@ -214,9 +217,9 @@ def show_processed_modules(dinstance, constants, mnames, mode):
"""
fig, ax = plt.subplots(1, figsize=(10, 10))
ax.set_axis_off()
- counter = 0
+ counter = 0 # Used as index within the `Noise` matrix, found in constants
- if 'AGIPD' in dinstance:
+ if dinstance in ('AGIPD1M1', 'AGIPD1M2'):
ax.set_xlim(0, 90)
ax.set_ylim(0, 75)
@@ -273,6 +276,62 @@ def show_processed_modules(dinstance, constants, mnames, mode):
elif mode == "processed":
ax.text(q_x[0] + 14.5, q_x[1] - q_st * im + 1.5,
f'Q{iq+1}M{im+1}', fontsize=24, color='gold')
+
+ elif dinstance == 'AGIPD500K':
+ # Create a dict that contains the range of tiles, in the figure,
+ # that belong to a module.
+ ranges = dict()
+ count = 0
+ for quadrant in range(1, 3):
+ for module in range(1, 5):
+ ranges[f'Q{quadrant}M{module}'] = [count, count + 8]
+ count += 8
+
+ geom = AGIPD_500K2GGeometry.from_origin()
+ ax = geom.inspect()
+
+ ax.set_title('') # Cannot remove title
+ ax.set_axis_off()
+ ax.get_legend().set_visible(False)
+ ax.figure.set_dpi(100)
+
+ # Remove non-tiles markings from figure
+ tiles, = ax.collections = ax.collections[:1]
+
+ # Set each tile colour individually
+ facecolors = tiles.get_facecolors().tolist() * 64
+
+ # Set module name fonts
+ for text in ax.texts:
+ text.set_fontweight('regular')
+
+ texts = [t for t in ax.texts if t.get_text() in mnames]
+ for text in texts:
+ text.set_fontweight('extra bold')
+ text.set_fontsize(14)
+
+ if mode == 'position': # Highlight selected modules
+ for module in mnames:
+ start, stop = ranges[module]
+ for idx in range(start, stop):
+ facecolors[idx] = colors.to_rgba('pink')
+
+ if mode == 'processed': # Highlight processed modules
+ for module, (start, stop) in ranges.items():
+ color = 'grey' # Unprocessed modules are grey
+
+ if module in mnames:
+ color = 'green'
+ if ('Noise' not in constants.keys() or
+ np.nanmean(constants['Noise'][counter, :, :, :, 0]) == 0): # noqa
+ color = 'red'
+ counter += 1
+
+ for idx in range(start, stop): # Set the colours
+ facecolors[idx] = colors.to_rgba(color)
+
+ tiles.set_facecolors(facecolors) # Update colours in figure
+
elif 'LPD' in dinstance:
ax.set_xlim(0, 97)
@@ -412,5 +471,5 @@ def show_processed_modules(dinstance, constants, mnames, mode):
_ = ax.legend(handles=[Patch(facecolor='red', label='No data'),
Patch(facecolor='gray', label='Not processed'),
Patch(facecolor='green', label='Processed')],
- loc='outside-top', ncol=3, bbox_to_anchor=(0.1, 0.25, 0.7, 0.8))
+ loc='best', ncol=3, bbox_to_anchor=(0.1, 0.25, 0.7, 0.8))
plt.show()
diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
index 5dc3a6c48990ee9e1ef68ad05dfc3f0bd9014668..c6bf10fa17e13457251c5cb641c9b3ec97778009 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
@@ -636,14 +636,12 @@
},
"outputs": [],
"source": [
- "# TODO: add show_processed_modules diagram for Mini-Half AGIPD\n",
- "if dinstance != \"AGIPD500K\":\n",
- " mnames=[]\n",
- " for i in modules:\n",
- " qm = f\"Q{i//4+1}M{i % 4+1}\"\n",
- " mnames.append(qm)\n",
- " display(Markdown(f'## Position of the module {qm} and it\\'s ASICs##'))\n",
- " show_processed_modules(dinstance, constants=None, mnames=mnames, mode=\"position\")"
+ "mnames=[]\n",
+ "for i in modules:\n",
+ " qm = f\"Q{i//4+1}M{i % 4+1}\"\n",
+ " mnames.append(qm)\n",
+ " display(Markdown(f'## Position of the module {qm} and its ASICs##'))\n",
+ "show_processed_modules(dinstance, constants=None, mnames=mnames, mode=\"position\")"
]
},
{
diff --git a/notebooks/generic/overallmodules_Darks_Summary_NBC.ipynb b/notebooks/generic/overallmodules_Darks_Summary_NBC.ipynb
index 5747928d6c6e309d653ed911767b1d142dc3f773..e829ab03d5cf621cce718c1b8880fe4e4c0e157a 100644
--- a/notebooks/generic/overallmodules_Darks_Summary_NBC.ipynb
+++ b/notebooks/generic/overallmodules_Darks_Summary_NBC.ipynb
@@ -253,10 +253,8 @@
},
"outputs": [],
"source": [
- "# TODO: add show_processed_modules diagram for Mini-Half AGIPD\n",
- "if dinstance != \"AGIPD500K\":\n",
- " display(Markdown('## Processed modules ##'))\n",
- " show_processed_modules(dinstance, constants, mod_names, mode=\"processed\")"
+ "display(Markdown('## Processed modules ##'))\n",
+ "show_processed_modules(dinstance, constants, mod_names, mode=\"processed\")"
]
},
{
diff --git a/requirements.txt b/requirements.txt
index ef5eb2bcafe7bb789943d452ce37dee6a7482a8f..37722e730835f2a7e3b20787b438e80234823b4d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,7 +6,7 @@ astsearch == 0.1.3
Cython == 0.29.21
dill == 0.3.0
extra_data == 1.2.0
-extra_geom == 0.8.0
+extra_geom == 1.0.0
fabio == 0.9.0
gitpython == 3.1.0
h5py == 2.10.0