import numpy as np
import matplotlib.gridspec as gridspec
from matplotlib import pyplot as plt
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
from matplotlib.figure import Figure
import iota.components.iota_misc as misc
import iota.components.iota_controls as ct
from iota.components.iota_utils import InputFinder
import prime.postrefine.mod_gui_dialogs as dlg
import prime.postrefine.mod_threads as thr
from prime.postrefine.mod_input import master_phil
ginp = InputFinder()
# Platform-specific stuff
# TODO: Will need to test this on Windows at some point
if wx.Platform == '__WXGTK__':
norm_font_size = 10
button_font_size = 12
LABEL_SIZE = 14
CAPTION_SIZE = 12
python = 'python'
elif wx.Platform == '__WXMAC__':
norm_font_size = 12
button_font_size = 14
LABEL_SIZE = 14
CAPTION_SIZE = 12
python = "Python"
def initialize_interface(self):
""" Initialize properties specific for command line
:return: True if successful, False if fails
"""
self.args, self.phil_args = parse_command_args(
self.iver, self.help_message).parse_known_args()
ginp = InputFinder()
# Check for type of input
if not self.args.path: # No input
parse_command_args(self.iver, self.help_message).print_help()
if self.args.default: # Write out default params and exit
help_out, txt_out = inp.print_params()
print('\n{:-^70}\n'.format('IOTA Parameters'))
print(help_out)
return False, 'IOTA_XTERM_INIT: OUTPUT PARAMETERS ONLY'
elif len(self.args.path) > 1: # If multiple paths / wildcards
file_list = ginp.make_input_list(self.args.path)
list_file = os.path.join(os.path.abspath(os.path.curdir),
'input.lst')
with open(list_file, 'w') as lf:
lf.write('\n'.join(file_list))
msg = "\nIOTA will run in AUTO mode using wildcard datapath:\n" \
"{} files found, compiled in {}\n".format(len(file_list), list_file)
self.iota_phil = inp.process_input(self.args, self.phil_args,
list_file, 'auto', self.now)
self.params = self.iota_phil.extract()
else: # If single path, check type
carg = os.path.abspath(self.args.path[0])
if os.path.isfile(carg):
ptype = ginp.get_file_type(carg)
if ptype.lower() in ('raw image', 'image pickle'):
msg = "\nIOTA will run in SINGLE-FILE mode using {}:\n".format(
carg)
mode = 'auto'
elif ('iota' and 'settings' in ptype.lower()):
msg = '\nIOTA will run in SCRIPT mode using {}:\n'.format(
carg)
mode = 'file'
elif 'list' in ptype.lower():
msg = "\nIOTA will run in AUTO mode using {}:\n".format(
carg)
mode = 'auto'
else:
pr = 'WARNING! File format not recognized. Proceed anyway? [Y/N] '
unknown_file = raw_input(pr)
if 'y' in unknown_file.lower():
ftype = raw_input(
"File type? [image, list, or parameters] ")
msg = "\nIOTA will run WITH DODGY input using {}:\n".format(
carg)
if 'par' in ftype:
mode = 'file'
else:
mode = 'auto'
else:
print('Exiting...')
return False, 'IOTA_XTERM_INIT_ERROR: Unrecognizable input!'
elif os.path.isdir(carg):
ptype = ginp.get_folder_type(carg)
if ('image' and 'folder' in ptype.lower()):
msg = "\nIOTA will run in AUTO mode using {}:\n".format(
carg)
mode = 'auto'
else:
msg = "IOTA_XTERM_INIT_ERROR: No images in {}!".format(
carg)
print(self.logo)
print(msg)
return False, msg
# If user provided gibberish
else:
msg = "IOTA_XTERM_INIT_ERROR: Invalid input! Need parameter filename " \
"or data folder."
print(self.logo)
print(msg)
return False, msg
# Initialize parameters for this command-line run
self.iota_phil = inp.process_input(self.args, self.phil_args, carg,
mode, self.now)
self.params = self.iota_phil.extract()
# Identify indexing / integration program and add to logo
b_end = " with {}".format(
str(self.params.advanced.processing_backend).upper())
prg = "{:>{w}}".format(b_end, w=76)
self.logo += prg
print(self.logo)
print('\n{}\n'.format(self.now))
if msg != '':
print(msg)
if self.args.analyze is not None:
print('ANALYSIS ONLY will be performed (analyzing run #{})'.format(
self.args.analyze))
self.analyze_prior_results('{:003d}'.format(int(
self.args.analyze)))
return False
if self.params.mp.method == 'mpi':
rank, size = get_mpi_rank_and_size()
self.master_process = rank == 0
else:
self.master_process = True
# Call function to read input folder structure (or input file) and
# generate list of image file paths
if self.params.cctbx_ha14.selection.select_only.flag_on:
cmd.Command.start("Importing saved grid search results")
self.gs_img_objects = self.make_int_object_list()
self.input_list = [i.conv_img for i in self.gs_img_objects]
cmd.Command.end("Importing saved grid search results -- DONE")
else:
cmd.Command.start("Reading input files")
self.input_list = self.make_input_list()
cmd.Command.end("Reading input files -- DONE")
# Select range of images/objects if turned on
if self.params.advanced.image_range.flag_on:
self.input_list = self.select_image_range(self.input_list)
# Pick a randomized subset of images/objects if turned on
if self.params.advanced.random_sample.flag_on and \
self.params.advanced.random_sample.number < len(self.input_list):
cmd.Command.start("Selecting {} random images out of {} found"
"".format(
self.params.advanced.random_sample.number,
len(self.input_list)))
self.input_list = self.select_random_subset(self.input_list)
cmd.Command.end(
"Selecting {} random images out of {} found -- DONE"
"".format(self.params.advanced.random_sample.number,
len(self.input_list)))
# Check for -l option, output list of input files and exit
if self.args.list:
list_file = os.path.abspath("{}/input.lst".format(os.curdir))
# Check if other files of this name exist under the current folder
list_folder = os.path.dirname(list_file)
list_files = [
i for i in os.listdir(list_folder) if i.endswith(".lst")
]
if len(list_files) > 0:
list_file = os.path.join(
list_folder, "input_{}.lst".format(len(list_files)))
msg = 'IOTA_XTERM_INIT: INPUT LIST ONLY option selected'
print('\n{}'.format(msg))
print('Input list in {} \n\n'.format(list_file))
with open(list_file, "w") as lf:
for i, input_file in enumerate(self.input_list, 1):
lf.write('{}\n'.format(input_file))
print("{}: {}".format(i, input_file))
lf.write('{}\n'.format(input_file))
print('\nExiting...\n\n')
return False, msg
return True, 'IOTA_XTERM_INIT: Initialization complete!'
