diff --git a/cfel_geom.py b/cfel_geom.py
index 0f5937e69ceded764be1da63bd84ad6a8e9f6acf..c1370d3390b5afcf3ba8b70fecfa262d159fa7da 100644
--- a/cfel_geom.py
+++ b/cfel_geom.py
@@ -25,6 +25,7 @@ from __future__ import print_function
from __future__ import unicode_literals
import numpy
+from cfel_crystfel import load_crystfel_geometry
def apply_geometry_from_file(data_as_slab, geometry_filename):
@@ -123,38 +124,6 @@ def pixel_maps_for_image_view(geometry_filename):
return yx, slab_shape, img_shape
-def parse_xy(string):
- """Extracts x and y values from strings in a geometry file.
-
- Parse the x, y values from strings in that have the format: '1x + 2.0y'.
-
- Args:
-
- string (str): the string to be parsed.
-
- Returns:
-
- x, y (float, float): the values of x and y.
- """
-
- x = y = 0
-
- if string.find('x') is not -1:
- xs = string.split('x')[0].split(' ')[-1]
- if len(xs) > 0:
- x = float(xs)
- else:
- x = 1.
-
- if string.find('y') is not -1:
- ys = string.split('y')[0].split(' ')[-1]
- if len(ys) > 0:
- y = float(ys)
- else:
- y = 1.
- return x, y
-
-
def pixel_maps_from_geometry_file(fnam):
"""Parses a geometry file and creates pixel maps.
@@ -172,122 +141,34 @@ def pixel_maps_from_geometry_file(fnam):
respectively x, y coordinates of the pixel and distance of the pixel from the center of the reference system.
"""
- f = open(fnam, 'r')
- f_lines = f.readlines()
- f.close()
+ detector = load_crystfel_geometry(fnam)
- keyword_list = ['min_fs', 'min_ss', 'max_fs', 'max_ss', 'fs', 'ss', 'corner_x', 'corner_y']
-
- detector_dict = {}
-
- panel_lines = [x for x in f_lines if '/' in x and
- len(x.split('/')) == 2 and x.split('/')[1].split('=')[0].strip() in keyword_list and
- 'bad_' not in x.split('/')[0].strip()]
-
- for pline in panel_lines:
- items = pline.split('=')[0].split('/')
- panel = items[0].strip()
- prop = items[1].strip()
- if prop in keyword_list:
- if panel not in detector_dict.keys():
- detector_dict[panel] = {}
- detector_dict[panel][prop] = pline.split('=')[1].split(';')[0]
-
- parsed_detector_dict = {}
-
- for p in detector_dict.keys():
-
- parsed_detector_dict[p] = {}
-
- parsed_detector_dict[p]['min_fs'] = int(detector_dict[p]['min_fs'])
- parsed_detector_dict[p]['max_fs'] = int(detector_dict[p]['max_fs'])
- parsed_detector_dict[p]['min_ss'] = int(detector_dict[p]['min_ss'])
- parsed_detector_dict[p]['max_ss'] = int(detector_dict[p]['max_ss'])
- parsed_detector_dict[p]['fs'] = list(parse_xy(detector_dict[p]['fs']))
- parsed_detector_dict[p]['ss'] = list(parse_xy(detector_dict[p]['ss']))
- parsed_detector_dict[p]['corner_x'] = float(detector_dict[p]['corner_x'])
- parsed_detector_dict[p]['corner_y'] = float(detector_dict[p]['corner_y'])
-
- max_slab_fs = numpy.array([parsed_detector_dict[k]['max_fs'] for k in parsed_detector_dict.keys()]).max()
- max_slab_ss = numpy.array([parsed_detector_dict[k]['max_ss'] for k in parsed_detector_dict.keys()]).max()
+ max_slab_fs = numpy.array([detector['panels'][k]['max_fs'] for k in detector['panels']]).max()
+ max_slab_ss = numpy.array([detector['panels'][k]['max_ss'] for k in detector['panels']]).max()
x = numpy.zeros((max_slab_ss+1, max_slab_fs+1), dtype=numpy.float32)
y = numpy.zeros((max_slab_ss+1, max_slab_fs+1), dtype=numpy.float32)
- for p in parsed_detector_dict.keys():
+ for p in detector['panels']:
# get the pixel coords for this asic
- i, j = numpy.meshgrid(numpy.arange(parsed_detector_dict[p]['max_ss'] - parsed_detector_dict[p]['min_ss'] + 1),
- numpy.arange(parsed_detector_dict[p]['max_fs'] - parsed_detector_dict[p]['min_fs'] + 1),
+ i, j = numpy.meshgrid(numpy.arange(detector['panels'][p]['max_ss'] - detector['panels'][p]['min_ss'] + 1),
+ numpy.arange(detector['panels'][p]['max_fs'] - detector['panels'][p]['min_fs'] + 1),
indexing='ij')
- #
# make the y-x ( ss, fs ) vectors, using complex notation
- dx = parsed_detector_dict[p]['fs'][1] + 1J * parsed_detector_dict[p]['fs'][0]
- dy = parsed_detector_dict[p]['ss'][1] + 1J * parsed_detector_dict[p]['ss'][0]
- r_0 = parsed_detector_dict[p]['corner_y'] + 1J * parsed_detector_dict[p]['corner_x']
+ dx = detector['panels'][p]['fsy'] + 1J * detector['panels'][p]['fsx']
+ dy = detector['panels'][p]['ssy'] + 1J * detector['panels'][p]['ssx']
+ r_0 = detector['panels'][p]['cny'] + 1J * detector['panels'][p]['cnx']
#
r = i * dy + j * dx + r_0
#
- y[parsed_detector_dict[p]['min_ss']: parsed_detector_dict[p]['max_ss'] + 1,
- parsed_detector_dict[p]['min_fs']: parsed_detector_dict[p]['max_fs'] + 1] = r.real
+ y[detector['panels'][p]['min_ss']: detector['panels'][p]['max_ss'] + 1,
+ detector['panels'][p]['min_fs']: detector['panels'][p]['max_fs'] + 1] = r.real
- x[parsed_detector_dict[p]['min_ss']: parsed_detector_dict[p]['max_ss'] + 1,
- parsed_detector_dict[p]['min_fs']: parsed_detector_dict[p]['max_fs'] + 1] = r.imag
+ x[detector['panels'][p]['min_ss']: detector['panels'][p]['max_ss'] + 1,
+ detector['panels'][p]['min_fs']: detector['panels'][p]['max_fs'] + 1] = r.imag
r = numpy.sqrt(numpy.square(x) + numpy.square(y))
return x, y, r
-
-def coffset_from_geometry_file(fnam):
- """Extracts detector distance information from a geometry file.
-
- Extracts detector distance offset information from a CrystFEL-style geometry file.
-
- Args:
-
- fnam (str): geometry filename.
-
- Returns:
-
- coffset (float): the detector distance offset
- """
-
- f = open(fnam, 'r')
- f_lines = f.readlines()
- f.close()
-
- coffset = 0.0
-
- for line in f_lines:
- if line.startswith('coffset'):
- coffset = float(line.split('=')[1].split(';')[0])
-
- return coffset
-
-
-def res_from_geometry_file(fnam):
- """Extracts pixel resolution information from a geometry file.
-
- Extracts pixel resolution information from a CrystFEL-style geometry file.
-
- Args:
-
- fnam (str): geometry filename.
-
- Returns:
-
- res (float): the pixel resolution
- """
-
- f = open(fnam, 'r')
- f_lines = f.readlines()
- f.close()
-
- res = None
-
- for line in f_lines:
- if line.startswith('res'):
- res = float(line.split('=')[1].split(';')[0])
-
- return res