def test_configure_parser_default():
parser = GooeyParser()
parser = configure_parser_default(parser)
dummy_input = ['/test/input/dir', '/test/output/dir',
'1', '2', '30.0', '300.0', '.lif']
args = parser.parse_args(dummy_input)
output = list(vars(args)).sort()
expected = ['input_directory',
'output_directory',
'glomeruli_channel_number',
'podocyte_channel_number',
'minimum_glomerular_diameter',
'maximum_glomerular_diameter',
'file_extension'].sort()
return output == expected
def main():
parser = GooeyParser(description='Example validator')
parser.add_argument('secret',
metavar='Super Secret Number',
help='A number specifically between 2 and 14',
gooey_options={
'validator': {
'test': '2 <= int(user_input) <= 14',
'message': 'Must be between 2 and 14'
}
})
args = parser.parse_args()
print("Cool! Your secret number is: ", args.secret)
def main():
import sys
print(sys.argv)
my_cool_parser = GooeyParser(description='Hai', add_help=False)
description_area = my_cool_parser.add_argument_group(
"Introduction",
long_intro,
gooey_options={
'show_border': False,
'show_underline': False,
}
)
# We need at least on
description_area.add_argument(
'-nothing',
gooey_options={
'visible': False,
}
)
categories = my_cool_parser.add_argument_group(
'Categories',
description='There are 13 species of crocodiles, so there are many different ' +
'sizes of crocodile. The smallest crocodile is the dwarf crocodile. ' +
'It grows to about 5.6 feet (1.7 meters) in length and weighs 13 to 15 pounds ',
gooey_options={
'show_border': False,
'label_color': '#FF9900',
'columns': 2,
# 'margin_top': 90
}
)
categories.add_argument(
'--parent-category',
metavar='Parent Category',
help='This is a very, very, very long help text '
'to explain a very, very, very important input value. '
'Unfortunately, the end of this long message is cropped. ',
choices=['a', 'b', 'c'],
required=True)
args = my_cool_parser.parse_args()
print("Hiya!")
def configure_parser():
"""Configure parser and add user input arguments.
Returns
-------
args : argparse arguments
Parsed user input arguments.
"""
parser = GooeyParser(prog='Podocyte Profiler', description=__DESCR__)
parser = configure_parser_default(parser)
args = parse_args(parser)
return args
def configure_parser():
"""Configure parser and add user input arguments.
Returns
-------
args : argparse arguments
Parsed user input arguments.
"""
parser = GooeyParser(prog='Podocyte Profiler', description=__DESCR__)
parser.add_argument('input_directory',
widget='DirChooser',
help='Folder containing files for processing.')
parser.add_argument('output_directory',
widget='DirChooser',
help='Folder to save output analysis files.')
parser.add_argument('number_of_image_channels',
help='Total number of color channels in image.',
type=int,
default=2)
return parser
def configure_parser():
"""Configure parser and add user input arguments.
Returns
-------
args : argparse arguments
Parsed user input arguments.
"""
parser = GooeyParser(prog='Podocyte Profiler', description=__DESCR__)
parser = configure_parser_default(parser)
parser.add_argument('xml_extension',
help='Extension of image file format (.xml)',
type=str,
default='.xml')
parser.add_argument('counts_directory',
widget='DirChooser',
help='Folder containing Fiji CellCounter files.')
args = parse_args(parser)
return args
def main():
import sys
print("sys.argv sys.argv sys.argv sys.argv sys.argv sys.argv")
print(sys.argv)
print('\n\n')
print(repr(sys.argv))
desc = "Example application to show Gooey's various widgets"
file_help_msg = "Name of the file you want to process"
my_cool_parser = GooeyParser(description=desc, add_help=False)
my_cool_parser.add_argument('thing',
default='.',
widget='MultiFileChooser',
help="asdfsadfasdfa sdfadf ad")
# my_cool_parser.add_argument(
# "region_name_list",
# help="Which regions do you want to run it for?",
# choices=['one' ,'two', 'three'],
# nargs="+",
# widget="Listbox",
# # widget='Counter'
# )
my_cool_parser.add_argument(
"FileChooser",
help=file_help_msg,
)
my_cool_parser.add_argument(
"Outfile",
widget='FileChooser',
metavar='Output Target',
help='Target output file',
gooey_options={'wildcard': 'Some Files (*.png)|*.png'}
# gooey_options={
# 'validator': {
# 'test': 'user_input == "foo"',
# 'message': 'Must be a valid filename'
# }
# }
)
my_cool_parser.add_argument(
'--listboxie',
metavar='Multiple selection',
nargs='+',
default=['Option three', 'Option four'],
choices=['Option one', 'Option two', 'Option three', 'Option four'],
help='Choose an action!',
widget='Listbox',
gooey_options={
'height': 500,
'validate': '',
'heading_color': '',
'text_color': '',
'hide_heading': True,
'hide_text': True,
})
#
search_options = my_cool_parser.add_argument_group(
'Search Options',
'Customize the search options',
gooey_options={
'show_border': True,
'columns': 2
})
x = search_options.add_argument('--query',
help='base search string'
# , gooey_options={'full_width': True}
)
search_options.add_argument('--other',
help='Another option in the search group'
# , gooey_options={'full_width': True}
)
search_options.add_argument('--one-more',
help='And another one'
# , gooey_options={'full_width': True}
)
search_flags = search_options.add_argument_group(
'Flags', gooey_options={'show_border': True})
search_flags.add_argument('--buy-it-now',
help="Will immediately purchase if possible",
action='store_true')
search_flags.add_argument('--auction',
help="Place bids up to PRICE_MAX",
action='store_true')
price_range = search_options.add_argument_group(
'Price_Range', gooey_options={'show_border': True})
price_range.add_argument('--price-min', help='min price')
price_range.add_argument('--price-max', help='max price')
foobar = search_options.add_mutually_exclusive_group(
gooey_options={
'title': 'Numeric Mutexes',
'show_border': False,
'label_color': '#00ff00'
})
foobar.add_argument('--one', help='oneie')
foobar.add_argument('--two', help='twoie')
foobar.add_argument('--three', help='twoie', action='store_true')
my_cool_parser.add_argument("DirChooser",
help=file_help_msg,
widget="DirChooser")
my_cool_parser.add_argument("FileSaver",
help=file_help_msg,
widget="FileSaver")
my_cool_parser.add_argument("MultiFileSaver",
help=file_help_msg,
widget="MultiFileChooser")
# my_cool_parser.add_argument("MultiDirSaver", help="Directories to open", widget='MultiDirChooser')
my_cool_parser.add_argument('-j',
'--jaws',
help='ooop',
widget="MultiFileChooser",
default="Yo yo!",
gooey_options={
'validator': {
'test': 'len(user_input) > 5',
'message': 'Must be over 5 chars!'
}
})
my_cool_parser.add_argument(
'-d',
'--duration',
default=2,
type=int,
help='Duration (in seconds) of the program output')
my_cool_parser.add_argument('-u',
'--textarea',
default="I'm on \na new line",
type=str,
help='A multiline textarea',
widget='Textarea',
gooey_options={'height': 100})
my_cool_parser.add_argument('-s',
'--cron-schedule',
type=int,
help='datetime when the cron should begin',
widget='DateChooser')
my_cool_parser.add_argument("-c",
"--showtime",
action="store_true",
help="display the countdown timer")
my_cool_parser.add_argument("-y",
"--yolo",
action="store_true",
widget='BlockCheckbox',
help="display the countdown timer")
my_cool_parser.add_argument("-p",
"--pause",
action="store_true",
help="Pause execution")
my_cool_parser.add_argument('-v', '--verbose', action='count')
my_cool_parser.add_argument("-o",
"--overwrite",
action="store_true",
default=True,
help="Overwrite output file (if present)")
my_cool_parser.add_argument('-r',
'--recursive',
choices=['yes', 'no'],
help='Recurse into subfolders')
# my_cool_parser.add_argument('-y', '--listboxie',
# nargs='+',
# choices=['hello', 'ay', 'yeah', 'boiiiii', 'wssup', 'longest', 'yeahhhboiii', 'ever'],
# help='Recurse into subfolders',
# widget='Listbox')
my_cool_parser.add_argument("-w",
"--writelog",
default="writelogs",
help="Dump output to local file")
my_cool_parser.add_argument("-e",
"--error",
action="store_true",
help="Stop process on error (default: No)")
verbosity = my_cool_parser.add_mutually_exclusive_group(required=False)
verbosity.add_argument('-t',
'--verbozze',
dest='verbose',
action='store_true',
help="Show more details")
verbosity.add_argument(
'-q',
'--quiet',
dest='quiet',
help="Only output on error",
# widget='DirChooser'
)
# my_cool_parser.add_argument('--sum', dest='accumulate', action='store_const',
# const=sum, default=max,
# help='sum the integers (default: find the max)')
import pprint
# stuff = [extract(x) for x in my_cool_parser._action_groups]
# mutex_groups = [group for group in my_cool_parser._mutually_exclusive_groups]
#
# pprint.pprint(reapply_mutex_groups(mutex_groups, stuff))
# my_cool_parser.print_help()
args = my_cool_parser.parse_args()
print(args)
# time.sleep(5)
print("Hiya!")
for i in range(20):
import time
print('Howdy', i)
time.sleep(.3)
def main():
# Get user input
parser = GooeyParser(prog='Podocyte Profiler', description=__DESCR__)
parser.add_argument('input_directory', widget='DirChooser', nargs='+',
help='Folder containing files for processing.')
parser.add_argument('output_directory', widget='DirChooser', nargs='+',
help='Folder to save output analysis files.')
parser.add_argument('glomeruli_channel_number', nargs='+',
help='Fluorescence channel with glomeruli.',
type=int, default=1)
parser.add_argument('podocyte_channel_number', nargs='+',
help='Fluorescence channel with podocytes.',
type=int, default=2)
parser.add_argument('minimum_glomerular_diameter', nargs='+',
help='Minimum glomerular diameter (microns).',
type=float, default=30)
parser.add_argument('maximum_glomerular_diameter', nargs='+',
help='Maximum glomerular diameter (microns).',
type=float, default=300)
parser.add_argument('file_extension', nargs='+',
help='Extension of image file format (.tif, etc.)',
type=str, default='.lif')
args = parser.parse_args()
input_directory = ' '.join(args.input_directory)
output_directory = ' '.join(args.output_directory)
channel_glomeruli = args.glomeruli_channel_number[0] - 1
channel_podocytes = args.podocyte_channel_number[0] - 1
min_glom_diameter = args.minimum_glomerular_diameter[0]
max_glom_diameter = args.maximum_glomerular_diameter[0]
ext = args.file_extension[0]
# Initialize
time_start = time.time()
timestamp = time.strftime('%d-%b-%Y_%H-%M%p', time.localtime())
log_file_begins(output_directory, args, timestamp)
detailed_stats = pd.DataFrame()
output_filename_detailed_stats = os.path.join(output_directory,
'Podocyte_detailed_stats_'+timestamp+'.csv')
# Get to work
filelist = find_files(input_directory, ext)
logging.info(f"{len(filelist)} {ext} files found.")
for filename in filelist:
logging.info(f"Processing file: {filename}")
try:
images = pims.open(filename)
except Exception:
continue
for im_series_num in range(images.metadata.ImageCount()):
logging.info(f"{images.metadata.ImageID(im_series_num)}")
logging.info(f"{images.metadata.ImageName(im_series_num)}")
images.series = im_series_num
images.bundle_axes = 'zyxc'
voxel_volume = images[0].metadata['mpp'] * \
images[0].metadata['mpp'] * \
images[0].metadata['mppZ']
glomeruli_labels = preprocess_glomeruli(images[0][..., channel_glomeruli])
glom_regions = filter_by_size(glomeruli_labels, min_glom_diameter, max_glom_diameter)
glom_index = 0 # glom labels will not always be sequential after filtering by size
logging.info(f"{len(glom_regions)} glomeruli identified.")
if len(glom_regions) > 0:
podocytes_view = denoise_image(images[0][..., channel_podocytes])
for glom in glom_regions:
podocyte_regions, centroid_offset, wshed = find_podocytes(
podocytes_view,
glom)
df = get_podocyte_statistics(podocyte_regions,
centroid_offset,
voxel_volume)
if df is None: continue
logging.info(f"{len(df)} podocytes found for this glomerulus. " +
f"Centroid (x,y,z): (" +
f"{int(glom.centroid[2])}, " +
f"{int(glom.centroid[1])}, " +
f"{int(glom.centroid[0])})")
df = get_podocyte_avg_statistics(df)
df = get_glom_statistics(df, glom, glom_index, voxel_volume)
df['image_series_num'] = images.metadata.ImageID(im_series_num)
df['image_series_name'] = images.metadata.ImageName(im_series_num)
df['image_filename'] = filename
detailed_stats = detailed_stats.append(df, ignore_index=True, sort=False)
detailed_stats.to_csv(output_filename_detailed_stats)
glom_index += 1
# Summarize output and write to file
summary_stats = create_summary_stats(detailed_stats)
output_filename_summary_stats = os.path.join(output_directory,
'Podocyte_summary_stats_'+timestamp+'.csv')
summary_stats.to_csv(output_filename_summary_stats)
logging.info(f'Saved statistics to file: {output_filename_summary_stats}')
total_gloms_counted = len(summary_stats)
log_file_ends(time_start, total_gloms_counted)
def main():
message = (
'Hi there!\n\n'
'Welcome to Gooey! \nThis is a demo of the flexible layouts and overall'
'customization you can achieve by using argument groups and '
'the new gooey_options feature.')
import sys
print(sys.argv)
desc = "Gooey transforms your CLI applications into beautiful GUIs!"
file_help_msg = "Name of the file you want to process"
my_cool_parser = GooeyParser(description=desc, add_help=False)
# categories = my_cool_parser.add_argument_group(
# 'Input Stage',
# gooey_options={
# 'show_border': True,
# # 'label_color': '#FF9900',
# 'columns': 2,
# # 'margin_top': 30
# }
# )
#
# categories.add_argument(
# '--subcategory',
# metavar='File',
# help='Path the audio file to encode.',
# widget='FileChooser',
# required=True,
# gooey_options={
# })
#
# categories.add_argument(
# '--subcategory21',
# metavar='File',
# help='Path the audio file to encode.',
# widget='FileChooser',
# required=True,
# gooey_options={
# })
# categories.add_argument(
# '--parent-category',
# metavar='Bitrate',
# help='The constant or variable bitrate (depending on codec choice)',
# choices=['a', 'b', 'c'],
# required=True,
# gooey_options={
# 'label_color': '#FF9900',
# 'label_bg_color': '#0000FF',
# # 'help_color': '#ff00ff',
# 'help_bg_color': '#ff00ff'
# })
search_options = my_cool_parser.add_argument_group(
'Output Stage',
'Specify the desired output behavior for the encoded file.',
gooey_options={
'show_border': True,
'columns': 2,
'margin_top': 25
})
search_options.add_argument(
'--query',
metavar="Output File",
help='The output destination for the encoded file',
widget='FileChooser',
gooey_options={'full_width': True})
#
search_flags = search_options.add_argument_group(
'Resampling', gooey_options={'show_border': True})
search_flags.add_argument(
'--buy-it-now',
metavar='Lowpass',
help="Frequency(kHz), lowpass filter cutoff above freq.",
action='store_true',
widget='BlockCheckbox',
gooey_options={'checkbox_label': 'Enable'})
search_flags.add_argument('--auction',
metavar='Resample',
help="Sampling frequency of output file(kHz)",
action='store_true',
widget='BlockCheckbox',
gooey_options={'checkbox_label': 'Enable'})
# price_range = search_options.add_argument_group('Price_Range',
# gooey_options={'show_border': True}
# )
#
# price_range.add_argument('--price-min',
# help='This'
# )
# price_range.add_argument(
# '--price-max',
# metavar='Priority',
# help='sets the process priority (Windows and OS/2-specific)',
# choices=[0,1,2,3,4],
# default=2
# )
my_cool_parser.print_help()
args = my_cool_parser.parse_args()
print(args)
print("Hiya!")
for i in range(20):
import time
print('Howdy', i)
time.sleep(.3)
def main():
import sys
print(sys.argv)
desc = "Example application to show Gooey's various widgets"
file_help_msg = "Name of the file you want to process"
parser = GooeyParser(description=desc, add_help=False)
# parser.add_argument('--textfield', default=2, widget="TextField", gooey_options={'full_width': True})
# parser.add_argument('--textarea', default="oneline twoline", widget='Textarea')
# parser.add_argument('--password', default="hunter42", widget='PasswordField')
# parser.add_argument('--commandfield', default="cmdr", widget='CommandField')
# parser.add_argument('--dropdown',
# choices=["one", "two"], default="two", widget='Dropdown')
# parser.add_argument('--listboxie',
# nargs='+',
# default=['Option three', 'Option four'],
# choices=['Option one', 'Option two', 'Option three',
# 'Option four'],
# widget='Listbox',
# gooey_options={
# 'height': 300,
# 'validate': '',
# 'heading_color': 'ff0000',
# 'text_color': '',
# 'hide_heading': False,
# 'hide_text': True,
# }
# )
# parser.add_argument('-c', '--counter', default=3, action='count', widget='Counter')
# #
# parser.add_argument("-o", "--overwrite", action="store_true",
# default=True,
# widget='CheckBox')
#
# ### Mutex Group ###
# verbosity = parser.add_mutually_exclusive_group(
# required=True,
# gooey_options={
# 'initial_selection': 1
# }
# )
# verbosity.add_argument(
# '--mutexone',
# default=True,
# action='store_true',
# help="Show more details")
#
# verbosity.add_argument(
# '--mutextwo',
# default='mut-2',
# widget='TextField')
parser.add_argument("--filechooser",
default="fc-value",
widget='FileChooser',
gooey_options={
'defaultFile': 'Sup n***a',
'message': 'Sup fam',
'wildcard': 'nig juice'
})
parser.add_argument("--filesaver", default="fs-value", widget='FileSaver')
parser.add_argument("--dirchooser",
default="dc-value",
widget='DirChooser')
parser.add_argument("--datechooser",
default="2015-01-01",
widget='DateChooser')
parser.add_argument("--multifilechooser",
default="2015-01-01",
widget='MultiFileChooser')
parser.add_argument("--multidirchooser",
default="2015-01-01",
widget='MultiDirChooser')
dest_vars = [
'textfield', 'textarea', 'password', 'commandfield', 'dropdown',
'listboxie', 'counter', 'overwrite', 'mutextwo', 'filechooser',
'filesaver', 'dirchooser', 'datechooser'
]
args = parser.parse_args()
for i in dest_vars:
assert getattr(args, i) is not None
print("Success")
def main():
message = (
'Hi there!\n\n'
'Welcome to Gooey! \nThis is a demo of the flexible layouts and overall'
'customization you can achieve by using argument groups and '
'the new gooey_options feature.')
import sys
print(sys.argv)
desc = "Example application to show Gooey's various widgets"
file_help_msg = "Name of the file you want to process"
my_cool_parser = GooeyParser(description=desc, add_help=False)
description_area = my_cool_parser.add_argument_group("About",
gooey_options={
'show_border':
True,
'show_underline':
False,
})
description_area.add_argument('thing',
default=message,
widget='Textarea',
help="asdfsadfasdfa sdfadf ad",
gooey_options={
'height': 100,
'show_help': False,
'show_label': False,
'readonly': True
})
categories = my_cool_parser.add_argument_group(
'Categories',
description=
'There are 13 species of crocodiles, so there are many different ' +
'sizes of crocodile. The smallest crocodile is the dwarf crocodile. ' +
'It grows to about 5.6 feet (1.7 meters) in length and weighs 13 to 15 pounds ',
gooey_options={
'show_border': False,
'label_color': '#FF9900',
'columns': 2,
# 'margin_top': 90
})
categories.add_argument(
'--parent-category',
metavar='Parent Category',
help='This is a very, very, very long help text '
'to explain a very, very, very important input value. '
'Unfortunately, the end of this long message is cropped. ',
choices=['a', 'b', 'c'],
required=True,
gooey_options={
'label_color': '#FF9900',
'label_bg_color': '#0000FF',
# 'help_color': '#ff00ff',
'help_bg_color': '#ff00ff'
})
categories.add_argument(
'--subcategory',
metavar='Subcategory',
help='Select Subcategory',
choices=['a', 'b', 'c'],
required=True,
gooey_options={
'label_color': '#FF9900',
'validator': {
'type':
'local',
'test':
'user_input',
'message':
'this is a super long error message wtih multiple ideas and suggestions on how to go about resolving the error '
}
# 'help_color': '#ff00ff',
# 'help_bg_color': '#ff0000'
})
search_options = my_cool_parser.add_argument_group(
'Search Options',
'Customize the search options',
gooey_options={
'show_border': True,
'columns': 2,
'margin_top': 25
})
search_options.add_argument('--query',
help='base search string',
gooey_options={'full_width': True})
#
search_flags = search_options.add_argument_group(
'Flags', gooey_options={'show_border': False})
search_flags.add_argument('--buy-it-now',
metavar='Buy it Now',
help="Will immediately purchase if possible",
action='store_true',
widget='BlockCheckbox',
gooey_options={
'label_color': '#4B5F83',
'checkbox_label': 'Enable'
})
search_flags.add_argument('--auction',
metavar='Auction',
help="Place bids up to PRICE_MAX",
action='store_true',
widget='BlockCheckbox',
gooey_options={
'label_color': '#4B5F83',
'checkbox_label': 'Enable'
})
price_range = search_options.add_argument_group(
'Price_Range', gooey_options={'show_border': True})
price_range.add_argument(
'--price-min',
help='This'
# 'is a very, very, very long help text '
# 'to explain a very, very, very important input value. '
)
price_range.add_argument('--price-max', help='max price')
args = my_cool_parser.parse_args()
print(args)
print("Hiya!")
for i in range(20):
import time
print('Howdy', i)
time.sleep(.3)
def main():
message = (
'Hi there!\n\n'
'Welcome to Gooey! \nThis is a demo of the flexible layouts and overall'
'customization you can achieve by using argument groups and '
'the new gooey_options feature.')
import sys
print(sys.argv)
desc = "Example application to show Gooey's various widgets"
file_help_msg = "Name of the file you want to process"
my_cool_parser = GooeyParser(description=desc, add_help=False)
categories = my_cool_parser.add_argument_group(
'Example 1',
description='This is the default group style',
gooey_options={
'show_underline': True,
'show_border': False,
# 'label_color': '#FF9900',
'columns': 1,
# 'margin_top': 90
})
categories.add_argument(
'--subcategoryasdf2asdf',
metavar='Parent Category',
help='Select Subcategory',
choices=['a', 'b', 'c'],
required=True,
)
categories.add_argument(
'--subcategory',
metavar='Subcategory',
help='Select Subcategory',
choices=['a', 'b', 'c'],
required=True,
)
categories1 = my_cool_parser.add_argument_group(
'Example 2',
description='This is an argument group with no horizontal line break',
gooey_options={
'show_underline': False,
'show_border': False,
})
categories1.add_argument(
'--subcategoryasdf2asdfasdf',
metavar='Parent Category',
help='Select Subcategory',
choices=['a', 'b', 'c'],
required=True,
)
categories1.add_argument(
'--subcategory1',
metavar='Subcategory',
help='Select Subcategory',
choices=['a', 'b', 'c'],
required=True,
)
categories2 = my_cool_parser.add_argument_group(
'Example 3',
description='This is an argument group with show_border = True',
gooey_options={
'show_underline': False,
'show_border': True,
# 'label_color': '#FF9900',
# 'columns': 2,
# 'margin_top': 90
})
categories2.add_argument(
'--subcategoryasdf2',
metavar='Parent Category',
help='Select Subcategory',
choices=['a', 'b', 'c'],
required=True,
)
categories2.add_argument(
'--subcategory2',
metavar='Subcategory',
help='Select Subcategory',
choices=['a', 'b', 'c'],
required=True,
)
my_cool_parser.print_help()
args = my_cool_parser.parse_args()
print(args)
print("Hiya!")
for i in range(20):
import time
print('Howdy', i)
time.sleep(.3)
