createLinkingScheme Namespace Reference

Classes
class	Layer
class	Pair

Functions
	parseArgs ()

Variables
	args = parseArgs()
	link_df = pd.read_csv(args.input_csv)
	link_df_orig_len = len(link_df)
	layer_from_idx = link_df['from'].values
	layer_to_idx = link_df['to'].values
	layer_idx = np.unique(np.concatenate((layer_from_idx, layer_to_idx)))
dict	layer_dict = {}
	dst_idx = link_df['from']
dict	l = layer_dict[idx]
dict	src_dict = {k: v for k, v in layer_dict.items() if v.nTargets == 0}
dict	dst_dict = {k: v for k, v in layer_dict.items() if v.nTargets > 0}
int	iter = 1
dict	pair_dict = {}
dict	dst_layer_dict = {}
dict	src_layer_dict = {}
	dst_df = link_df[link_df['to'] == key]
	dst_vec = dst_df['from']
list	missing_links = []
int	src_vol = p1.src // 10000
int	dst_vol = p1.dst // 10000
int	skip = 8
int	src_rem1 = p1.src % 10000
int	dst_rem1 = p1.dst % 10000
bool	isPaired = False
int	src_rem2 = p2.src % 10000
int	dst_rem2 = p2.dst % 10000
int	new_src = -1
int	new_dst = -1
int	nConnsTotal = 0
	link_file = open(args.write_scheme_file, 'w')
	bin_table = open(args.output_file, 'w')
int	conn_counter = 0

Function Documentation

parseArgs()

createLinkingScheme.parseArgs

(

)

Definition at line 5 of file createLinkingScheme.py.

def parseArgs():
    import argparse
    parser = argparse.ArgumentParser(description="create GBTS linking table")
    parser.add_argument("-o", "--output_file", default="binTables_ITK_RUN4.txt", help="output table for use by GBTS (default=%(default)s)")
    parser.add_argument("-p", "--min-link-probability", type=float, default=0.01, help="minimum linking probability (default=%(default)s, LRT=0.001)")
    parser.add_argument("-e", "--eta-bins", type=float, default=0.2, help="eta bin width (default=%(default)s)")
    parser.add_argument("-a", "--no-symmetrize", action='store_true', help="do not symmetrize by adding missing layers on the other side")
    parser.add_argument("-i", "--write-inverse-linking-scheme", action='store_true', help="write inverse linking scheme table")
    parser.add_argument("-w", "--write-scheme-file", default="inverse_linking_scheme_ITK_RUN4.txt", help="inverse linking scheme table file name (default=%(default)s)")
    parser.add_argument("input_csv", nargs="?", default="layer_connection_table.csv", help="input CSV layer connection table, output from Athena (default=%(default)s)")
    return parser.parse_args()
 

Variable Documentation

args

createLinkingScheme.args = parseArgs()

Definition at line 29 of file createLinkingScheme.py.

bin_table

createLinkingScheme.bin_table = open(args.output_file, 'w')

Definition at line 170 of file createLinkingScheme.py.

conn_counter

int createLinkingScheme.conn_counter = 0

Definition at line 174 of file createLinkingScheme.py.

dst_df

createLinkingScheme.dst_df = link_df[link_df['to'] == key]

Definition at line 80 of file createLinkingScheme.py.

dst_dict

dict createLinkingScheme.dst_dict = {k: v for k, v in layer_dict.items() if v.nTargets > 0}

Definition at line 59 of file createLinkingScheme.py.

dst_idx

createLinkingScheme.dst_idx = link_df['from']

Definition at line 52 of file createLinkingScheme.py.

dst_layer_dict

dict createLinkingScheme.dst_layer_dict = {}

Definition at line 65 of file createLinkingScheme.py.

dst_rem1

int createLinkingScheme.dst_rem1 = p1.dst % 10000

Definition at line 114 of file createLinkingScheme.py.

dst_rem2

int createLinkingScheme.dst_rem2 = p2.dst % 10000

Definition at line 122 of file createLinkingScheme.py.

dst_vec

createLinkingScheme.dst_vec = dst_df['from']

Definition at line 81 of file createLinkingScheme.py.

dst_vol

int createLinkingScheme.dst_vol = p1.dst // 10000

Definition at line 108 of file createLinkingScheme.py.

isPaired

bool createLinkingScheme.isPaired = False

Definition at line 116 of file createLinkingScheme.py.

iter

int createLinkingScheme.iter = 1

Definition at line 62 of file createLinkingScheme.py.

l

dict createLinkingScheme.l = layer_dict[idx]

Definition at line 55 of file createLinkingScheme.py.

layer_dict

dict createLinkingScheme.layer_dict = {}

Definition at line 47 of file createLinkingScheme.py.

layer_from_idx

createLinkingScheme.layer_from_idx = link_df['from'].values

Definition at line 40 of file createLinkingScheme.py.

layer_idx

createLinkingScheme.layer_idx = np.unique(np.concatenate((layer_from_idx, layer_to_idx)))

Definition at line 43 of file createLinkingScheme.py.

layer_to_idx

createLinkingScheme.layer_to_idx = link_df['to'].values

Definition at line 41 of file createLinkingScheme.py.

link_df

createLinkingScheme.link_df = pd.read_csv(args.input_csv)

Definition at line 33 of file createLinkingScheme.py.

link_df_orig_len

createLinkingScheme.link_df_orig_len = len(link_df)

Definition at line 34 of file createLinkingScheme.py.

link_file

createLinkingScheme.link_file = open(args.write_scheme_file, 'w')

Definition at line 159 of file createLinkingScheme.py.

missing_links

list createLinkingScheme.missing_links = []

Definition at line 98 of file createLinkingScheme.py.

nConnsTotal

int createLinkingScheme.nConnsTotal = 0

Definition at line 153 of file createLinkingScheme.py.

new_dst

int createLinkingScheme.new_dst = -1

Definition at line 139 of file createLinkingScheme.py.

new_src

int createLinkingScheme.new_src = -1

Definition at line 130 of file createLinkingScheme.py.

pair_dict

dict createLinkingScheme.pair_dict = {}

Definition at line 64 of file createLinkingScheme.py.

skip

int createLinkingScheme.skip = 8

Definition at line 110 of file createLinkingScheme.py.

src_dict

dict createLinkingScheme.src_dict = {k: v for k, v in layer_dict.items() if v.nTargets == 0}

Definition at line 58 of file createLinkingScheme.py.

src_layer_dict

dict createLinkingScheme.src_layer_dict = {}

Definition at line 66 of file createLinkingScheme.py.

src_rem1

int createLinkingScheme.src_rem1 = p1.src % 10000

Definition at line 113 of file createLinkingScheme.py.

src_rem2

int createLinkingScheme.src_rem2 = p2.src % 10000

Definition at line 121 of file createLinkingScheme.py.

src_vol

int createLinkingScheme.src_vol = p1.src // 10000

Definition at line 107 of file createLinkingScheme.py.