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Commit d6142d51 authored by Cyril Danilevski's avatar Cyril Danilevski :scooter:
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Make use of extra geom for report figures

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cal_tools/cal_tools/plotting.py
+ 79
− 238
View file @ d6142d51
from pathlib import Path
from typing import Any, Dict, Optional
from extra_geom import AGIPD_500K2GGeometry
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import colors
from matplotlib.patches import Patch, Rectangle
from matplotlib.patches import Patch
from mpl_toolkits.axes_grid1 import AxesGrid
import numpy as np
from extra_geom import (AGIPD_1MGeometry, AGIPD_500K2GGeometry,
DSSC_1MGeometry, LPD_1MGeometry)
from extra_geom import tests as eg_tests
def show_overview(d, cell_to_preview, gain_to_preview, out_folder=None, infix=None):
......@@ -215,258 +219,95 @@ def show_processed_modules(dinstance: str, constants: Optional[Dict[str, Any]],
"processed": To show the modules successfully processed.
:return
"""
fig, ax = plt.subplots(1, figsize=(10, 10))
ax.set_axis_off()
counter = 0 # Used as index within the `Noise` matrix, found in constants
if dinstance in ('AGIPD1M1', 'AGIPD1M2'):
# Create the geometry figure for each detector
ax.set_xlim(0, 90)
ax.set_ylim(0, 75)
asic_pos = 5
q_st = 8
# quad_pos = [Q1[x, y], Q2[x, y], Q3[x, y], Q4[x, y]]
quad_pos = [[43, 66], [45, 34], [4, 32], [2, 64]]
l_y = 6
l_x = 5
for iq, q_x in enumerate(quad_pos):
for im in range(4):
if mode == "processed":
color = 'gray'
ecolor = 'darkgreen'
if f'Q{iq+1}M{im+1}' in mnames:
color = 'green'
if 'Noise' not in constants.keys() or \
np.nanmean(constants['Noise'][counter, :, :, :, 0]) == 0: # noqa
color = 'red'
counter += 1
else:
color = 'lightblue'
ecolor = 'c'
x = q_x[0]
for _ in range(8):
# adding modules patches
ax.add_patch(Rectangle((x, q_x[1] - q_st * im), 5, 6,
linewidth=2, edgecolor=ecolor,
facecolor=color, fill=True))
if mode == "position":
if f"Q{iq+1}M{im+1}" in mnames:
ax.add_patch(
Rectangle((x, q_x[1] - q_st * im),
l_x, l_y / 2, linewidth=2,
edgecolor='c',
facecolor='sandybrown',
fill=True))
ax.add_patch(
Rectangle((x, (q_x[1] - q_st * im + 3)),
l_x, l_y / 2, linewidth=2,
edgecolor='c',
facecolor='sandybrown',
fill=True))
x += asic_pos
if mode == "position":
if f"Q{iq+1}M{im+1}" in mnames:
# Change Text for current processed module.
ax.text(q_x[0] + 13, q_x[1] - q_st * im + 1.5,
f'Q{iq+1}M{im+1}', fontsize=28,
color='mediumblue', weight='bold')
else:
ax.text(q_x[0] + 14, q_x[1] - q_st * im + 1.5,
f'Q{iq+1}M{im+1}', fontsize=25, color='k')
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')
if dinstance in ('AGIPD1M1', 'AGIPD1M2'):
quadrants = 4
modules = 4
tiles = 8
quad_pos = [(-525, 625), (-550, -10), (520, -160), (542.5, 475)]
geom = AGIPD_1MGeometry.from_quad_positions(quad_pos)
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
quadrants = 2
modules = 4
tiles = 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)
elif 'LPD' in dinstance:
quadrants = 4
modules = 4
tiles = 16
quad_pos = [(11.4, 299), (-11.5, 8), (254.5, -16), (278.5, 275)]
geom = LPD_1MGeometry.from_quad_positions(quad_pos)
# Remove non-tiles markings from figure
tiles, = ax.collections = ax.collections[:1]
elif 'DSSC' in dinstance:
quadrants = 4
modules = 4
tiles = 2
quad_pos = [(-130, 5), (-130, -125), (5, -125), (5, 5)]
geom = DSSC_1MGeometry.from_h5_file_and_quad_positions(
Path(eg_tests.__file__).parent / 'dssc_geo_june19.h5',
quad_pos)
else:
raise ValueError(f'{dinstance} is not a real detector')
# Create a dict that contains the range of tiles, in the figure,
# that belong to a module.
ranges = dict()
tile_count = 0
for quadrant in range(1, quadrants+1):
for module in range(1, modules+1):
ranges[f'Q{quadrant}M{module}'] = [tile_count, tile_count + tiles]
tile_count += tiles
# Create the figure
ax = geom.inspect()
ax.set_title('') # Cannot remove title
ax.set_axis_off()
ax.get_legend().set_visible(False)
# Set each tile colour individually
facecolors = tiles.get_facecolors().tolist() * 64
# Remove non-tiles markings from figure
tiles, = ax.collections = ax.collections[:1]
# Set module name fonts
for text in ax.texts:
text.set_fontweight('regular')
# Set each tile colour individually, extra_geom provides a single color
# for all tiles.
facecolors = tiles.get_facecolor() * tile_count
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)
# Set module name fonts
for text in ax.texts:
text.set_fontweight('regular')
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')
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 == 'processed': # Highlight processed modules
for module, (start, stop) in ranges.items():
color = 'grey' # Unprocessed modules are grey
if mode == 'position': # Highlight selected modules
for module in mnames:
start, stop = ranges[module]
facecolors[start:stop] = colors.to_rgba('pink')
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
else: # mode == 'processed': Highlight processed modules
counter = 0 # Used as index within the `Noise` matrix
for module, (start, stop) in ranges.items():
color = 'grey' # Unprocessed modules are grey
for idx in range(start, stop): # Set the colours
facecolors[idx] = colors.to_rgba(color)
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
tiles.set_facecolors(facecolors) # Update colours in figure
for idx in range(start, stop): # Set the colours
facecolors[idx] = colors.to_rgba(color)
elif 'LPD' in dinstance:
tiles.set_facecolors(facecolors) # Update colours in figure
ax.set_xlim(0, 97)
ax.set_ylim(0, 97)
q_poses = np.array([[51, 47], [47, 1], [1, 5], [5, 51]])
m_poses = np.array([[22.5, 20.5], [22.5, 0.5],
[0.5, 0.5], [0.5, 20.5]])
for iq, q_pos in enumerate(q_poses):
ax.add_patch(Rectangle(q_pos, 45, 45, linewidth=2,
edgecolor='darkgreen',
facecolor='cornsilk', fill=True))
ax.text(q_pos[0] + 20, q_pos[1] + 41.5, f'Q{iq+1}', fontsize=22)
for im, m_pos in enumerate(m_poses):
if mode == "processed":
color = 'gray'
ecolor = 'darkgreen'
if f'Q{iq+1}M{im+1}' in mnames:
color = 'green'
if 'Noise' not in constants.keys() or \
np.nanmean(constants['Noise'][counter, :, :, :, 0]) == 0: # noqa
color = 'red'
counter += 1
pos = q_pos + m_pos + np.array([5, 8])
ax.text(pos[0], pos[1], f'Q{iq+1}M{im+1}',
fontsize=24, color='gold')
elif mode == "position":
color = 'lightblue'
ecolor = 'c'
# adding modules patches
ax.add_patch(Rectangle(q_pos + m_pos, 22, 20, linewidth=3,
edgecolor=ecolor, facecolor=color,
fill=True))
if mode == "position":
if f"Q{iq+1}M{im+1}" in mnames:
for a_posx in range(2):
for a_posy in range(8):
a_pos = np.array([a_posx*11., a_posy*20/8.])
pos = q_pos + m_pos + a_pos
# Top Asics patches
ax.add_patch(Rectangle(q_pos+m_pos+a_pos, 11,
20/8., linewidth=1,
edgecolor='k',
facecolor='sandybrown',
fill=True))
if a_posx == 0:
label = str(a_posy + 9)
else:
label = str(-a_posy + (a_posx * 8))
ax.text(pos[0] + 4, pos[1] + 0.3, label,
fontsize=14)
else:
pos = q_pos + m_pos + np.array([5, 8])
ax.text(pos[0], pos[1], f'Q{iq+1}M{im+1}',
fontsize=22, color='k')
if mode == "position":
ax.add_patch(Rectangle([65, 93], 30, 4, linewidth=1,
edgecolor='k', facecolor='sandybrown',
fill=True))
ax.text(52, 94, 'ASICs:', fontsize=22, color='k')
for i_pos in range(8):
pos = np.array([65, 93]) + np.array([i_pos*30/8.+0.3, 0.3]) # noqa
ax.add_patch(Rectangle(pos, 24/8., 3.4, linewidth=1,
edgecolor='k',
facecolor='sandybrown',
fill=True))
ax.text(pos[0]+0.5, pos[1]+0.5, f'{i_pos+1}',
fontsize=18, color='k')
elif 'DSSC' in dinstance:
ax.set_xlim(0, 85)
ax.set_ylim(0, 79)
asic_pos = 20
q_st = 8
# quad_pos = [Q1[x, y], Q2[x, y], Q3[x, y], Q4[x, y]]
quad_pos = [[45, 64], [43, 24], [0, 28], [0, 66]]
mod_ind = [[4, 3, 2, 1], [4, 3, 2, 1], [1, 2, 3, 4], [1, 2, 3, 4]]
for iq, q_x in enumerate(quad_pos):
for im in range(4):
if mode == "processed":
color = 'gray'
ecolor = 'darkgreen'
if f'Q{iq+1}M{mod_ind[iq][im]}' in mnames:
color = 'green'
if 'Noise' not in constants.keys() or \
np.nanmean(constants['Noise'][counter, :, :, :]) == 0: # noqa
color = 'red'
counter += 1
else:
color = 'lightblue'
ecolor = 'c'
x = q_x[0]
for _ in range(2):
# adding modules patches
ax.add_patch(Rectangle((x, q_x[1] - q_st * im), 19, 10,
linewidth=2, edgecolor=ecolor,
facecolor=color, fill=True))
if mode == "position":
# Check if it is the processed module to highlight.
if f"Q{iq+1}M{mod_ind[iq][im]}" in mnames:
ax.add_patch(Rectangle((x, q_x[1] - q_st * im),
19, 10, linewidth=2,
edgecolor='c',
facecolor="sandybrown",
fill=True))
ax.text(q_x[0] + 2, q_x[1] - q_st * im + 4.5,
'T1 T2', fontsize=18, # noqa
color='grey')
x += asic_pos
if mode == "position":
# Check if it is the processed module to highlight.
if f'Q{iq+1}M{mod_ind[iq][im]}' in mnames:
# Change Text for current processed module.
ax.text(q_x[0] + 12.7, q_x[1] - q_st * im + 4.5,
f'Q{iq + 1} M{mod_ind[iq][im]}', fontsize=26,
color='mediumblue', weight='bold')
else:
ax.text(q_x[0] + 13.5, q_x[1] - q_st * im + 4.5,
f'Q{iq+1} M{mod_ind[iq][im]}',
fontsize=25, color='k')
elif mode == "processed":
ax.text(q_x[0] + 13.5, q_x[1] - q_st * im + 4.5,
f'Q{iq+1} M{mod_ind[iq][im]}', fontsize=24,
color='gold')
ax.text(q_x[0] + 2, q_x[1] - q_st * im + 4.5,
'T1 T2', fontsize=18,
color='y')
if mode == "processed":
_ = ax.legend(handles=[Patch(facecolor='red', label='No data'),
Patch(facecolor='gray', label='Not processed'),
......
tests/test_cal_tools.py
+ 10
− 0
View file @ d6142d51
......@@ -2,9 +2,19 @@ from datetime import datetime
from pathlib import Path
import pytest
from cal_tools.plotting import show_processed_modules
from cal_tools.tools import get_dir_creation_date
def test_show_processed_modules():
mnames = ['Q1M1']
with pytest.raises(ValueError) as err:
show_processed_modules('LDP', mnames=mnames,
constants={}, mode='processed')
assert 'LDP' in err.value()
def test_dir_creation_date():
folder = '/gpfs/exfel/exp/DETLAB/202031/p900172/raw'
......
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