diff --git a/crystfel_utils.py b/crystfel_utils.py
index 01aa3b673b830961412bc6744bc311757e117de9..63566103b3082637e756d089abe04b358453c5a2 100644
--- a/crystfel_utils.py
+++ b/crystfel_utils.py
@@ -13,17 +13,11 @@
# You should have received a copy of the GNU General Public License
# along with cfelpyutils. If not, see <http://www.gnu.org/licenses/>.
"""
-Utilities for interoperability with data formats used in the CrystFEL
-software package.
+CryystFEL utilities.
-Exports:
-
- Functions:
-
- load_crystfel_geometry: a python reimplementation of the
- get_detector_geometry_2 function from CrystFEL.
+This module contains the implementation of several functions used to
+interact with CrystFEL files and data (geometry files, stream files).
"""
-
from __future__ import (absolute_import, division, print_function,
unicode_literals)
diff --git a/geometry_utils.py b/geometry_utils.py
index 6265cff6e47f34af77e74e6c25b6bacccd827daa..c280f73154e9438c071e33ba66683b0044c7c319 100644
--- a/geometry_utils.py
+++ b/geometry_utils.py
@@ -13,23 +13,10 @@
# You should have received a copy of the GNU General Public License
# along with cfelpyutils. If not, see <http://www.gnu.org/licenses/>.
"""
-Utilities to load, manipulate and apply geometry information to
-detector pixel data.
+Geometry utilities.
-Exports:
-
- Functions:
-
- compute_pix_maps: turn a CrystFEL geometry object into pixel
- maps.
-
- compute_min_array_size: compute the minimum array size that
- is required to store data to which a geometry has been
- applied.
-
- compute_visualization_pix_maps: ajust pixel maps to be used in
- a PyQtGraph's ImageView widget.
-"""
+This module contains the implementation of several functions used to
+manipulate geometry information."""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
@@ -75,33 +62,29 @@ def compute_pix_maps(geometry):
PixelMaps: A PixelMaps tuple storing the pixel maps (ndarrays
of type float).
"""
- # Determine the max fs and ss in the geometry object.
- max_slab_fs = numpy.array([
+ max_fs_in_slab = numpy.array([
geometry['panels'][k]['max_fs']
for k in geometry['panels']
]).max()
- max_slab_ss = numpy.array([
+ max_ss_in_slab = numpy.array([
geometry['panels'][k]['max_ss']
for k in geometry['panels']
]).max()
- # Create empty arrays, of the same size of the input data, that
- # will store the x and y pixel maps.
x_map = numpy.zeros(
- shape=(max_slab_ss + 1, max_slab_fs + 1),
+ shape=(max_ss_in_slab + 1, max_fs_in_slab + 1),
dtype=numpy.float32 # pylint: disable=E1101
)
y_map = numpy.zeros(
- shape=(max_slab_ss + 1, max_slab_fs + 1),
+ shape=(max_ss_in_slab + 1, max_fs_in_slab + 1),
dtype=numpy.float32 # pylint: disable=E1101
)
# Iterate over the panels. For each panel, determine the pixel
# indices, then compute the x,y vectors. Finally, copy the
# panel pixel maps into the detector-wide pixel maps.
- # At the end, compute the values for the radius pixel map.
for pan in geometry['panels']:
ss_grid, fs_grid = numpy.meshgrid(
numpy.arange(
@@ -178,7 +161,6 @@ def compute_min_array_size(pixel_maps):
y_minimum = 2 * int(max(abs(y_map.max()), abs(y_map.min()))) + 2
x_minimum = 2 * int(max(abs(x_map.max()), abs(x_map.min()))) + 2
- # Return a numpy-style tuple with the computed shape.
return (y_minimum, x_minimum)
@@ -204,12 +186,10 @@ def compute_visualization_pix_maps(geometry):
coordinates (as ndarrays of type int). The third field
("r") is just set to None.
"""
- # Essentially, the origin of the reference system needs to be
- # moved from the beam position to the top-left of the image that
- # will be displayed. First, compute the normal pixel maps, then
- # compute the size of the array used to display the data, finally
- # use this information to estimate the magnitude of the shift that
- # needs to be applied to the origin of the system.
+ # Shift the origin of the reference system from the beam position
+ # to the top-left of the image that will be displayed. Compute the
+ # size of the array needed to display the data, then use this
+ # information to estimate the magnitude of the shift.
pixel_maps = compute_pix_maps(geometry)
min_shape = compute_min_array_size(pixel_maps)
new_x_map = numpy.array(
diff --git a/parameter_utils.py b/parameter_utils.py
index 18c33be74e374d8a8c0eb6276bf995dc016453e6..dd5a0392320be2fb50f69e2e4b788e19bcb5347c 100644
--- a/parameter_utils.py
+++ b/parameter_utils.py
@@ -13,17 +13,11 @@
# You should have received a copy of the GNU General Public License
# along with cfelpyutils. If not, see <http://www.gnu.org/licenses/>.
"""
-Utilities for parsing command line options and configuration files.
+Parameter parsing utilities.
-Exports:
-
- Functions:
-
- convert_parameters: convert a dictionary returned by the
- configparse module to a dictionary containing entries with
- the correct type.
+This module contains the implementation of several utilities used
+to parse and manipulate dictionaries that store options and parameters.
"""
-
from __future__ import (absolute_import, division, print_function,
unicode_literals)
@@ -91,16 +85,8 @@ def convert_parameters(config_dict):
monitor_params = {}
- # Iterate over the sections in the dictionary (first level in the
- # configuration file). Add the section to the dictionary that will
- # be returned.
for section in config_dict.keys():
monitor_params[section] = {}
-
- # Iterate then over the content of the section (second level in
- # the configuration file). Get each option in turn and perform
- # all the checks. If all checks fail, call the parsing_error
- # function.
for option in config_dict[section].keys():
recovered_option = config_dict[section][option]
if (