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acutesoftware/AIKIF | aikif/web_app/page_search.py | search_aikif | def search_aikif(txt, formatHTML=True):
"""
search for text - currently this looks in all folders in the
root of AIKIF but that also contains binaries so will need to
use the agent_filelist.py to specify the list of folders.
NOTE - this needs to use indexes rather than full search each time
... | python | def search_aikif(txt, formatHTML=True):
"""
search for text - currently this looks in all folders in the
root of AIKIF but that also contains binaries so will need to
use the agent_filelist.py to specify the list of folders.
NOTE - this needs to use indexes rather than full search each time
... | [
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acutesoftware/AIKIF | aikif/web_app/page_search.py | format_result | def format_result(line, line_num, txt):
""" highlight the search result """
return ' ' + str(line_num) + ': ' + line.replace(txt, '<span style="background-color: #FFFF00">' + txt + '</span>') | python | def format_result(line, line_num, txt):
""" highlight the search result """
return ' ' + str(line_num) + ': ' + line.replace(txt, '<span style="background-color: #FFFF00">' + txt + '</span>') | [
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acutesoftware/AIKIF | aikif/environments/happiness.py | TEST | def TEST():
"""
Modules for testing happiness of 'persons' in 'worlds'
based on simplistic preferences. Just a toy - dont take seriously
----- WORLD SUMMARY for : Mars -----
population = 0
tax_rate = 0.0
tradition = 0.9
equity = 0.0
Preferences for Rov... | python | def TEST():
"""
Modules for testing happiness of 'persons' in 'worlds'
based on simplistic preferences. Just a toy - dont take seriously
----- WORLD SUMMARY for : Mars -----
population = 0
tax_rate = 0.0
tradition = 0.9
equity = 0.0
Preferences for Rov... | [
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tax_rate = 0.0
tradition = 0.9
equity = 0.0
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acutesoftware/AIKIF | aikif/environments/happiness.py | WorldFinder.solve | def solve(self, max_worlds=10000, silent=False):
"""
find the best world to make people happy
"""
self.num_worlds = 0
num_unhappy = 0
for tax_rate in range(self.tax_range[0],self.tax_range[1]):
for equity in range(self.equity_range[0],self.equity_range[1]):
... | python | def solve(self, max_worlds=10000, silent=False):
"""
find the best world to make people happy
"""
self.num_worlds = 0
num_unhappy = 0
for tax_rate in range(self.tax_range[0],self.tax_range[1]):
for equity in range(self.equity_range[0],self.equity_range[1]):
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acutesoftware/AIKIF | aikif/environments/happiness.py | Happiness.show_details | def show_details(self):
"""
extended print details of happiness parameters
"""
res = str(self)
res += '\nDETAILS\n'
for f in self.factors:
res += str(f)
return res | python | def show_details(self):
"""
extended print details of happiness parameters
"""
res = str(self)
res += '\nDETAILS\n'
for f in self.factors:
res += str(f)
return res | [
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acutesoftware/AIKIF | aikif/environments/happiness.py | Value.match_value_to_text | def match_value_to_text(self, text):
"""
this is going to be the tricky bit - probably not possible
to get the 'exact' rating for a value. Will need to do sentiment
analysis of the text to see how it matches the rating. Even that
sounds like it wont work - maybe a ML algorithm wo... | python | def match_value_to_text(self, text):
"""
this is going to be the tricky bit - probably not possible
to get the 'exact' rating for a value. Will need to do sentiment
analysis of the text to see how it matches the rating. Even that
sounds like it wont work - maybe a ML algorithm wo... | [
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acutesoftware/AIKIF | aikif/web_app/web_utils.py | list2html | def list2html(lst):
"""
convert a list to html using table formatting
"""
txt = '<TABLE width=100% border=0>'
for l in lst:
txt += '<TR>\n'
if type(l) is str:
txt+= '<TD>' + l + '</TD>\n'
elif type(l) is list:
txt+= '<TD>'
for i in l:
... | python | def list2html(lst):
"""
convert a list to html using table formatting
"""
txt = '<TABLE width=100% border=0>'
for l in lst:
txt += '<TR>\n'
if type(l) is str:
txt+= '<TD>' + l + '</TD>\n'
elif type(l) is list:
txt+= '<TD>'
for i in l:
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acutesoftware/AIKIF | aikif/web_app/web_utils.py | build_edit_form | def build_edit_form(title, id, cols, return_page):
"""
returns the html for a simple edit form
"""
txt = '<H3>' + title + '<H3>'
txt += '<form action="' + return_page + '" method="POST">\n' # return_page = /agents
txt += ' updating id:' + str(id) + '\n<BR>'
txt += ' <input type="hidden" ... | python | def build_edit_form(title, id, cols, return_page):
"""
returns the html for a simple edit form
"""
txt = '<H3>' + title + '<H3>'
txt += '<form action="' + return_page + '" method="POST">\n' # return_page = /agents
txt += ' updating id:' + str(id) + '\n<BR>'
txt += ' <input type="hidden" ... | [
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acutesoftware/AIKIF | aikif/web_app/web_utils.py | build_html_listbox | def build_html_listbox(lst, nme):
"""
returns the html to display a listbox
"""
res = '<select name="' + nme + '" multiple="multiple">\n'
for l in lst:
res += ' <option>' + str(l) + '</option>\n'
res += '</select>\n'
return res | python | def build_html_listbox(lst, nme):
"""
returns the html to display a listbox
"""
res = '<select name="' + nme + '" multiple="multiple">\n'
for l in lst:
res += ' <option>' + str(l) + '</option>\n'
res += '</select>\n'
return res | [
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acutesoftware/AIKIF | aikif/web_app/web_utils.py | build_data_list | def build_data_list(lst):
"""
returns the html with supplied list as a HTML listbox
"""
txt = '<H3>' + List + '<H3><UL>'
for i in lst:
txt += '<LI>' + i + '</LI>'
txt += '<UL>'
return txt | python | def build_data_list(lst):
"""
returns the html with supplied list as a HTML listbox
"""
txt = '<H3>' + List + '<H3><UL>'
for i in lst:
txt += '<LI>' + i + '</LI>'
txt += '<UL>'
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acutesoftware/AIKIF | aikif/web_app/web_utils.py | filelist2html | def filelist2html(lst, fldr, hasHeader='N'):
"""
formats a standard filelist to htmk using table formats
"""
txt = '<TABLE width=100% border=0>'
numRows = 1
if lst:
for l in lst:
if hasHeader == 'Y':
if numRows == 1:
td_begin = '<TH>'
... | python | def filelist2html(lst, fldr, hasHeader='N'):
"""
formats a standard filelist to htmk using table formats
"""
txt = '<TABLE width=100% border=0>'
numRows = 1
if lst:
for l in lst:
if hasHeader == 'Y':
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td_begin = '<TH>'
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acutesoftware/AIKIF | aikif/web_app/web_utils.py | link_file | def link_file(f, fldr):
"""
creates a html link for a file using folder fldr
"""
fname = os.path.join(fldr,f)
if os.path.isfile(fname):
return '<a href="/aikif/data/core/' + f + '">' + f + '</a>'
else:
return f | python | def link_file(f, fldr):
"""
creates a html link for a file using folder fldr
"""
fname = os.path.join(fldr,f)
if os.path.isfile(fname):
return '<a href="/aikif/data/core/' + f + '">' + f + '</a>'
else:
return f | [
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acutesoftware/AIKIF | aikif/web_app/web_utils.py | dict_to_htmlrow | def dict_to_htmlrow(d):
"""
converts a dictionary to a HTML table row
"""
res = "<TR>\n"
for k, v in d.items():
if type(v) == str:
res = res + '<TD><p>' + k + ':</p></TD><TD><p>' + v + '</p></TD>'
else:
res = res + '<TD><p>' + k + ':</p></TD><TD><p>' + str(v) ... | python | def dict_to_htmlrow(d):
"""
converts a dictionary to a HTML table row
"""
res = "<TR>\n"
for k, v in d.items():
if type(v) == str:
res = res + '<TD><p>' + k + ':</p></TD><TD><p>' + v + '</p></TD>'
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acutesoftware/AIKIF | aikif/web_app/web_utils.py | read_csv_to_html_table | def read_csv_to_html_table(csvFile, hasHeader='N'):
"""
reads a CSV file and converts it to HTML
"""
txt = '<table class="as-table as-table-zebra as-table-horizontal">'
with open(csvFile, "r") as f: #
numRows = 1
for row in f:
if hasHeader == 'Y':
if num... | python | def read_csv_to_html_table(csvFile, hasHeader='N'):
"""
reads a CSV file and converts it to HTML
"""
txt = '<table class="as-table as-table-zebra as-table-horizontal">'
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acutesoftware/AIKIF | aikif/web_app/web_utils.py | read_csv_to_html_list | def read_csv_to_html_list(csvFile):
"""
reads a CSV file and converts it to a HTML List
"""
txt = ''
with open(csvFile) as csv_file:
for row in csv.reader(csv_file, delimiter=','):
txt += '<div id="table_row">'
for col in row:
txt += " "
... | python | def read_csv_to_html_list(csvFile):
"""
reads a CSV file and converts it to a HTML List
"""
txt = ''
with open(csvFile) as csv_file:
for row in csv.reader(csv_file, delimiter=','):
txt += '<div id="table_row">'
for col in row:
txt += " "
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acutesoftware/AIKIF | aikif/agents/explore/agent_explore_grid.py | ExploreAgent.do_your_job | def do_your_job(self):
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acutesoftware/AIKIF | aikif/agents/explore/agent_explore_grid.py | ExploreAgent.lg_mv | def lg_mv(self, log_lvl, txt):
"""
wrapper for debugging print and log methods
"""
if log_lvl <= self.LOG_LEVEL:
print(txt + str(self.current_y) + "," + str(self.current_x)) | python | def lg_mv(self, log_lvl, txt):
"""
wrapper for debugging print and log methods
"""
if log_lvl <= self.LOG_LEVEL:
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acutesoftware/AIKIF | aikif/agents/explore/agent_explore_grid.py | ExploreAgent.get_intended_direction | def get_intended_direction(self):
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"""
x = 0
y = 0
if self.target_x == self.current_x and self.target_y == self.current_y:
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acutesoftware/AIKIF | aikif/agents/explore/agent_explore_grid.py | ExploreAgent.show_status | def show_status(self):
"""
dumps the status of the agent
"""
txt = 'Agent Status:\n'
print(txt)
txt += "start_x = " + str(self.start_x) + "\n"
txt += "start_y = " + str(self.start_y) + "\n"
txt += "target_x = " + str(self.target_x) + "\n"
txt += ... | python | def show_status(self):
"""
dumps the status of the agent
"""
txt = 'Agent Status:\n'
print(txt)
txt += "start_x = " + str(self.start_x) + "\n"
txt += "start_y = " + str(self.start_y) + "\n"
txt += "target_x = " + str(self.target_x) + "\n"
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acutesoftware/AIKIF | aikif/toolbox/audio_tools.py | get_audio_metadata_old | def get_audio_metadata_old(fname):
""" retrieve the metadata from an MP3 file """
audio_dict = {}
print("IDv2 tag info for %s:" % fname)
try:
audio = mutagenx.id3.ID3(fname, translate=False)
except StandardError as err:
print("ERROR = " + str(err))
#else:
#print(audio.ppr... | python | def get_audio_metadata_old(fname):
""" retrieve the metadata from an MP3 file """
audio_dict = {}
print("IDv2 tag info for %s:" % fname)
try:
audio = mutagenx.id3.ID3(fname, translate=False)
except StandardError as err:
print("ERROR = " + str(err))
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Nachtfeuer/pipeline | spline/tools/table.py | calculate_columns | def calculate_columns(sequence):
"""
Find all row names and the maximum column widths.
Args:
columns (dict): the keys are the column name and the value the max length.
Returns:
dict: column names (key) and widths (value).
"""
columns = {}
for row in sequence:
for k... | python | def calculate_columns(sequence):
"""
Find all row names and the maximum column widths.
Args:
columns (dict): the keys are the column name and the value the max length.
Returns:
dict: column names (key) and widths (value).
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columns = {}
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Nachtfeuer/pipeline | spline/tools/table.py | calculate_row_format | def calculate_row_format(columns, keys=None):
"""
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Args:
columns (dict): the keys are the column name and the value the max length.
keys (list): optional list of keys to order columns as well as to filter for them.
Returns:
str: format for table row
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"""
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Args:
columns (dict): the keys are the column name and the value the max length.
keys (list): optional list of keys to order columns as well as to filter for them.
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Nachtfeuer/pipeline | spline/tools/table.py | pprint | def pprint(sequence, keys=None):
"""
Print sequence as ascii table to stdout.
Args:
sequence (list or tuple): a sequence with a dictionary each entry.
keys (list): optional list of keys to order columns as well as to filter for them.
"""
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"""
Print sequence as ascii table to stdout.
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sequence (list or tuple): a sequence with a dictionary each entry.
keys (list): optional list of keys to order columns as well as to filter for them.
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Nachtfeuer/pipeline | spline/matrix.py | matrix_worker | def matrix_worker(data):
"""
Run pipelines in parallel.
Args:
data(dict): parameters for the pipeline (model, options, ...).
Returns:
dict: with two fields: success True/False and captured output (list of str).
"""
matrix = data['matrix']
Logger.get_logger(__name__ + '.worke... | python | def matrix_worker(data):
"""
Run pipelines in parallel.
Args:
data(dict): parameters for the pipeline (model, options, ...).
Returns:
dict: with two fields: success True/False and captured output (list of str).
"""
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Nachtfeuer/pipeline | spline/matrix.py | Matrix.can_process_matrix | def can_process_matrix(entry, matrix_tags):
"""
Check given matrix tags to be in the given list of matric tags.
Args:
entry (dict): matrix item (in yaml).
matrix_tags (list): represents --matrix-tags defined by user in command line.
Returns:
bool: Tru... | python | def can_process_matrix(entry, matrix_tags):
"""
Check given matrix tags to be in the given list of matric tags.
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entry (dict): matrix item (in yaml).
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Nachtfeuer/pipeline | spline/matrix.py | Matrix.run_matrix_ordered | def run_matrix_ordered(self, process_data):
"""
Running pipelines one after the other.
Returns
dict: with two fields: success True/False and captured output (list of str).
"""
output = []
for entry in self.matrix:
env = entry['env'].copy()
... | python | def run_matrix_ordered(self, process_data):
"""
Running pipelines one after the other.
Returns
dict: with two fields: success True/False and captured output (list of str).
"""
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Nachtfeuer/pipeline | spline/matrix.py | Matrix.run_matrix_in_parallel | def run_matrix_in_parallel(self, process_data):
"""Running pipelines in parallel."""
worker_data = [{'matrix': entry, 'pipeline': process_data.pipeline,
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"""Running pipelines in parallel."""
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Nachtfeuer/pipeline | spline/matrix.py | Matrix.process | def process(self, process_data):
"""Process the pipeline per matrix item."""
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return self.run_matrix_in_parallel(process_data)
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aartur/mschematool | mschematool/core.py | _sqlfile_to_statements | def _sqlfile_to_statements(sql):
"""
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"""
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aartur/mschematool | mschematool/core.py | MigrationsRepository.generate_migration_name | def generate_migration_name(self, name, suffix):
"""Returns a name of a new migration. It will usually be a filename with
a valid and unique name.
:param name: human-readable name of a migration
:param suffix: file suffix (extension) - eg. 'sql'
"""
return os.path.join(s... | python | def generate_migration_name(self, name, suffix):
"""Returns a name of a new migration. It will usually be a filename with
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:param name: human-readable name of a migration
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"""
args = [connection_param]
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acutesoftware/AIKIF | aikif/dataTools/cls_data.py | Data._identify_datatype | def _identify_datatype(self, input_data):
"""
uses the input data, which may be a string, list, number
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"""
if isinstance(input_data, (int, float)) :
... | python | def _identify_datatype(self, input_data):
"""
uses the input data, which may be a string, list, number
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acutesoftware/AIKIF | aikif/dataTools/cls_data.py | Data._calc_size_stats | def _calc_size_stats(self):
"""
get the size in bytes and num records of the content
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self.total_records = 0
self.total_length = 0
self.total_nodes = 0
if type(self.content['data']) is dict:
self.total_length += len(str(self.content['data']))
... | python | def _calc_size_stats(self):
"""
get the size in bytes and num records of the content
"""
self.total_records = 0
self.total_length = 0
self.total_nodes = 0
if type(self.content['data']) is dict:
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staticdev/django-pagination-bootstrap | pagination_bootstrap/version.py | _make_version | def _make_version(major, minor, micro, releaselevel, serial):
"""Create a readable version string from version_info tuple components."""
assert releaselevel in ['alpha', 'beta', 'candidate', 'final']
version = "%d.%d" % (major, minor)
if micro:
version += ".%d" % (micro,)
if releaselevel != ... | python | def _make_version(major, minor, micro, releaselevel, serial):
"""Create a readable version string from version_info tuple components."""
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staticdev/django-pagination-bootstrap | pagination_bootstrap/version.py | _make_url | def _make_url(major, minor, micro, releaselevel, serial):
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url = "https://django-pagination-bootstrap.readthedocs.io"
if releaselevel != 'final':
# For pre-releases, use a version-specific URL.
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acutesoftware/AIKIF | aikif/lib/cls_filelist.py | FileList.get_list_of_paths | def get_list_of_paths(self):
"""
return a list of unique paths in the file list
"""
all_paths = []
for p in self.fl_metadata:
try:
all_paths.append(p['path'])
except:
try:
print('cls_filelist - ... | python | def get_list_of_paths(self):
"""
return a list of unique paths in the file list
"""
all_paths = []
for p in self.fl_metadata:
try:
all_paths.append(p['path'])
except:
try:
print('cls_filelist - ... | [
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acutesoftware/AIKIF | aikif/lib/cls_filelist.py | FileList.add_file_metadata | def add_file_metadata(self, fname):
"""
collects the files metadata - note that this will fail
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acutesoftware/AIKIF | aikif/lib/cls_filelist.py | FileList.print_file_details_as_csv | def print_file_details_as_csv(self, fname, col_headers):
""" saves as csv format """
line = ''
qu = '"'
d = ','
for fld in col_headers:
if fld == "fullfilename":
line = line + qu + fname + qu + d
if fld == "name":
l... | python | def print_file_details_as_csv(self, fname, col_headers):
""" saves as csv format """
line = ''
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acutesoftware/AIKIF | aikif/lib/cls_filelist.py | FileList.save_filelist | def save_filelist(self, opFile, opFormat, delim=',', qu='"'):
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uses a List of files and collects meta data on them and saves
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op_folder = os.path.dirname(opFile)
if op_folder is not None: # ... | python | def save_filelist(self, opFile, opFormat, delim=',', qu='"'):
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acutesoftware/AIKIF | aikif/dataTools/cls_dataset.py | DataSet.login | def login(self, schema, username, password):
"""
connect here - use the other classes cls_oracle, cls_mysql, etc
otherwise this has the credentials used to access a share folder
"""
self.schema = schema
self.username = username
self.password = password
sel... | python | def login(self, schema, username, password):
"""
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Phelimb/atlas | mykatlas/typing/typer/presence.py | GeneCollectionTyper.type | def type(self, sequence_coverage_collection,
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"""Types a collection of genes returning the most likely gene version
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best_versions = self.get_best_version(
sequence_coverage_collection.values(... | python | def type(self, sequence_coverage_collection,
min_gene_percent_covg_threshold=99):
"""Types a collection of genes returning the most likely gene version
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acutesoftware/AIKIF | aikif/programs.py | Programs.list_all_python_programs | def list_all_python_programs(self):
"""
collects a filelist of all .py programs
"""
self.tot_lines = 0
self.tot_bytes = 0
self.tot_files = 0
self.tot_loc = 0
self.lstPrograms = []
fl = mod_fl.FileList([self.fldr], ['*.py'], ["__pycache__", "/venv/"... | python | def list_all_python_programs(self):
"""
collects a filelist of all .py programs
"""
self.tot_lines = 0
self.tot_bytes = 0
self.tot_files = 0
self.tot_loc = 0
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acutesoftware/AIKIF | aikif/programs.py | Programs.save | def save(self, fname=''):
"""
Save the list of items to AIKIF core and optionally to local file fname
"""
if fname != '':
with open(fname, 'w') as f:
for i in self.lstPrograms:
f.write(self.get_file_info_line(i, ','))
# sa... | python | def save(self, fname=''):
"""
Save the list of items to AIKIF core and optionally to local file fname
"""
if fname != '':
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gets details on the program, size, date, list of functions
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mpg-age-bioinformatics/AGEpy | AGEpy/david.py | id_nameDAVID | def id_nameDAVID(df,GTF=None,name_id=None):
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"""
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mpg-age-bioinformatics/AGEpy | AGEpy/david.py | DAVIDgetGeneAttribute | def DAVIDgetGeneAttribute(x,df,refCol="ensembl_gene_id",fieldTOretrieve="gene_name"):
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Nachtfeuer/pipeline | spline/tools/loc/application.py | main | def main(**options):
"""Spline loc tool."""
application = Application(**options)
# fails application when your defined threshold is higher than your ratio of com/loc.
if not application.run():
sys.exit(1)
return application | python | def main(**options):
"""Spline loc tool."""
application = Application(**options)
# fails application when your defined threshold is higher than your ratio of com/loc.
if not application.run():
sys.exit(1)
return application | [
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"""Loading configuration."""
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Nachtfeuer/pipeline | spline/tools/loc/application.py | Application.ignore_path | def ignore_path(path):
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pattern (str): regex to search for line commens and block comments
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mpg-age-bioinformatics/AGEpy | AGEpy/biom.py | datasetsBM | def datasetsBM(host=biomart_host):
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Lists BioMart datasets.
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:returns: nothing
"""
stdout_ = sys.stdout #Keep track of the previous value.
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Lists BioMart datasets.
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acutesoftware/AIKIF | aikif/core_data.py | CoreData.format_csv | def format_csv(self, delim=',', qu='"'):
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Prepares the data in CSV format
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acutesoftware/AIKIF | aikif/core_data.py | CoreData.get_child_by_name | def get_child_by_name(self, name):
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find the child object by name and return the object
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for c in self.child_nodes:
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return c
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acutesoftware/AIKIF | aikif/core_data.py | CoreTable.get_filename | def get_filename(self, year):
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returns the filename
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res = self.fldr + os.sep + self.type + year + '.' + self.user
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returns the filename
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acutesoftware/AIKIF | aikif/core_data.py | CoreTable.save | def save(self, file_tag='2016', add_header='N'):
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"""
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save table to folder in appropriate files
NOTE - ONLY APPEND AT THIS STAGE - THEN USE DATABASE
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Prepares the header in CSV format
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extracts event information from core tables into diary files
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"""
extracts event information from core tables into diary files
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print('Generate diary files from Event rows only')
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Nachtfeuer/pipeline | spline/components/ansible.py | Ansible.creator | def creator(entry, config):
"""Creator function for creating an instance of an Ansible script."""
ansible_playbook = "ansible.playbook.dry.run.see.comment"
ansible_inventory = "ansible.inventory.dry.run.see.comment"
ansible_playbook_content = render(config.script, model=config.model, en... | python | def creator(entry, config):
"""Creator function for creating an instance of an Ansible script."""
ansible_playbook = "ansible.playbook.dry.run.see.comment"
ansible_inventory = "ansible.inventory.dry.run.see.comment"
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acutesoftware/AIKIF | aikif/toolbox/cls_grid_life.py | GameOfLife.update_gol | def update_gol(self):
"""
Function that performs one step of the Game of Life
"""
updated_grid = [[self.update_cell(row, col) \
for col in range(self.get_grid_width())] \
for row in range(self.get_grid_height())]
... | python | def update_gol(self):
"""
Function that performs one step of the Game of Life
"""
updated_grid = [[self.update_cell(row, col) \
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acutesoftware/AIKIF | aikif/toolbox/cls_grid_life.py | GameOfLife.update_cell | def update_cell(self, row, col):
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Function that computes the update for one cell in the Game of Life
"""
# compute number of living neighbors
neighbors = self.eight_neighbors(row, col)
living_neighbors = 0
for neighbor in neighbors:
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"""
Function that computes the update for one cell in the Game of Life
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acutesoftware/AIKIF | aikif/toolbox/cls_grid_life.py | GameOfLifePatterns.random_offset | def random_offset(self, lst):
"""
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res = []
x = random.randint(4,self.max_x - 42)
y = random.randint(4,self.max_y - 10)
for itm in lst:
res.append([itm[0] + y, itm[1] +... | python | def random_offset(self, lst):
"""
offsets a pattern list generated below to a random
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res = []
x = random.randint(4,self.max_x - 42)
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JelleAalbers/multihist | multihist.py | Hist1d.get_random | def get_random(self, size=10):
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JelleAalbers/multihist | multihist.py | Hist1d.std | def std(self, bessel_correction=True):
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if bessel_correction:
n = self.n
bc = n / (n - 1)
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bc = 1
return np.sqrt(np.average((self.bin_centers - se... | python | def std(self, bessel_correction=True):
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n = self.n
bc = n / (n - 1)
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JelleAalbers/multihist | multihist.py | Histdd._data_to_hist | def _data_to_hist(self, data, **kwargs):
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JelleAalbers/multihist | multihist.py | Histdd.bin_centers | def bin_centers(self, axis=None):
"""Return bin centers along an axis, or if axis=None, list of bin_centers along each axis"""
if axis is None:
return np.array([self.bin_centers(axis=i) for i in range(self.dimensions)])
axis = self.get_axis_number(axis)
return 0.5 * (self.bin... | python | def bin_centers(self, axis=None):
"""Return bin centers along an axis, or if axis=None, list of bin_centers along each axis"""
if axis is None:
return np.array([self.bin_centers(axis=i) for i in range(self.dimensions)])
axis = self.get_axis_number(axis)
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JelleAalbers/multihist | multihist.py | Histdd.get_axis_bin_index | def get_axis_bin_index(self, value, axis):
"""Returns index along axis of bin in histogram which contains value
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"""
axis = self.get_axis_number(axis)
bin_edges = self.bin_edges[axis]
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"""Returns index along axis of bin in histogram which contains value
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JelleAalbers/multihist | multihist.py | Histdd.get_bin_indices | def get_bin_indices(self, values):
"""Returns index tuple in histogram of bin which contains value"""
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for ax_i in range(self.dimensions)]) | python | def get_bin_indices(self, values):
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JelleAalbers/multihist | multihist.py | Histdd.all_axis_bin_centers | def all_axis_bin_centers(self, axis):
"""Return ndarray of same shape as histogram containing bin center value along axis at each point"""
# Arcane hack that seems to work, at least in 3d... hope
axis = self.get_axis_number(axis)
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"""Return ndarray of same shape as histogram containing bin center value along axis at each point"""
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axis = self.get_axis_number(axis)
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JelleAalbers/multihist | multihist.py | Histdd.sum | def sum(self, axis):
"""Sums all data along axis, returns d-1 dimensional histogram"""
axis = self.get_axis_number(axis)
if self.dimensions == 2:
new_hist = Hist1d
else:
new_hist = Histdd
return new_hist.from_histogram(np.sum(self.histogram, axis=axis),
... | python | def sum(self, axis):
"""Sums all data along axis, returns d-1 dimensional histogram"""
axis = self.get_axis_number(axis)
if self.dimensions == 2:
new_hist = Hist1d
else:
new_hist = Histdd
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JelleAalbers/multihist | multihist.py | Histdd.slicesum | def slicesum(self, start, stop=None, axis=0):
"""Slices the histogram along axis, then sums over that slice, returning a d-1 dimensional histogram"""
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JelleAalbers/multihist | multihist.py | Histdd.projection | def projection(self, axis):
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axis = self.get_axis_number(axis)
projected_hist = np.sum(self.histogram, axis=self.other_axes(axis))
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"""Sums all data along all other axes, then return Hist1D"""
axis = self.get_axis_number(axis)
projected_hist = np.sum(self.histogram, axis=self.other_axes(axis))
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JelleAalbers/multihist | multihist.py | Histdd.cumulate | def cumulate(self, axis):
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JelleAalbers/multihist | multihist.py | Histdd.central_likelihood | def central_likelihood(self, axis):
"""Returns new histogram with all values replaced by their central likelihoods along axis."""
result = self.cumulative_density(axis)
result.histogram = 1 - 2 * np.abs(result.histogram - 0.5)
return result | python | def central_likelihood(self, axis):
"""Returns new histogram with all values replaced by their central likelihoods along axis."""
result = self.cumulative_density(axis)
result.histogram = 1 - 2 * np.abs(result.histogram - 0.5)
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JelleAalbers/multihist | multihist.py | Histdd.lookup_hist | def lookup_hist(self, mh):
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This is not rebinning: no interpolation /renormalization is performed.
It's just a lookup.
"""
result = mh.similar_blank_histogram()
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acutesoftware/AIKIF | scripts/examples/doc_roadmap.py | create_roadmap_doc | def create_roadmap_doc(dat, opFile):
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takes a dictionary read from a yaml file and converts
it to the roadmap documentation
"""
op = format_title('Roadmap for AIKIF')
for h1 in dat['projects']:
op += format_h1(h1)
if dat[h1] is None:
op += '(No details)\n'
... | python | def create_roadmap_doc(dat, opFile):
"""
takes a dictionary read from a yaml file and converts
it to the roadmap documentation
"""
op = format_title('Roadmap for AIKIF')
for h1 in dat['projects']:
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acutesoftware/AIKIF | aikif/toolbox/cls_grid.py | Grid.clear | def clear(self):
"""
Clears grid to be EMPTY
"""
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"""
Clears grid to be EMPTY
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acutesoftware/AIKIF | aikif/toolbox/cls_grid.py | Grid.save | def save(self, fname):
""" saves a grid to file as ASCII text """
try:
with open(fname, "w") as f:
f.write(str(self))
except Exception as ex:
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""" saves a grid to file as ASCII text """
try:
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f.write(str(self))
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acutesoftware/AIKIF | aikif/toolbox/cls_grid.py | Grid.extract_col | def extract_col(self, col):
"""
get column number 'col'
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new_col = [row[col] for row in self.grid]
return new_col | python | def extract_col(self, col):
"""
get column number 'col'
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get row number 'row'
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... | get row number 'row' | [
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acutesoftware/AIKIF | aikif/toolbox/cls_grid.py | Grid.replace_row | def replace_row(self, line, ndx):
"""
replace a grids row at index 'ndx' with 'line'
"""
for col in range(len(line)):
self.set_tile(ndx, col, line[col]) | python | def replace_row(self, line, ndx):
"""
replace a grids row at index 'ndx' with 'line'
"""
for col in range(len(line)):
self.set_tile(ndx, col, line[col]) | [
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acutesoftware/AIKIF | aikif/toolbox/cls_grid.py | Grid.replace_col | def replace_col(self, line, ndx):
"""
replace a grids column at index 'ndx' with 'line'
"""
for row in range(len(line)):
self.set_tile(row, ndx, line[row]) | python | def replace_col(self, line, ndx):
"""
replace a grids column at index 'ndx' with 'line'
"""
for row in range(len(line)):
self.set_tile(row, ndx, line[row]) | [
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acutesoftware/AIKIF | aikif/toolbox/cls_grid.py | Grid.new_tile | def new_tile(self, num=1):
"""
Create a new tile in a randomly selected empty
square. The tile should be 2 90% of the time and
4 10% of the time.
"""
for _ in range(num):
if random.random() > .5:
new_tile = self.pieces[0]
... | python | def new_tile(self, num=1):
"""
Create a new tile in a randomly selected empty
square. The tile should be 2 90% of the time and
4 10% of the time.
"""
for _ in range(num):
if random.random() > .5:
new_tile = self.pieces[0]
... | [
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acutesoftware/AIKIF | aikif/toolbox/cls_grid.py | Grid.set_tile | def set_tile(self, row, col, value):
"""
Set the tile at position row, col to have the given value.
"""
#print('set_tile: y=', row, 'x=', col)
if col < 0:
print("ERROR - x less than zero", col)
col = 0
#return
if col > s... | python | def set_tile(self, row, col, value):
"""
Set the tile at position row, col to have the given value.
"""
#print('set_tile: y=', row, 'x=', col)
if col < 0:
print("ERROR - x less than zero", col)
col = 0
#return
if col > s... | [
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acutesoftware/AIKIF | aikif/toolbox/cls_grid.py | Grid.replace_grid | def replace_grid(self, updated_grid):
"""
replace all cells in current grid with updated grid
"""
for col in range(self.get_grid_width()):
for row in range(self.get_grid_height()):
if updated_grid[row][col] == EMPTY:
self.set_empty(row, col... | python | def replace_grid(self, updated_grid):
"""
replace all cells in current grid with updated grid
"""
for col in range(self.get_grid_width()):
for row in range(self.get_grid_height()):
if updated_grid[row][col] == EMPTY:
self.set_empty(row, col... | [
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acutesoftware/AIKIF | aikif/toolbox/cls_grid.py | Grid.find_safe_starting_point | def find_safe_starting_point(self):
"""
finds a place on the grid which is clear on all sides
to avoid starting in the middle of a blockage
"""
y = random.randint(2,self.grid_height-4)
x = random.randint(2,self.grid_width-4)
return y, x | python | def find_safe_starting_point(self):
"""
finds a place on the grid which is clear on all sides
to avoid starting in the middle of a blockage
"""
y = random.randint(2,self.grid_height-4)
x = random.randint(2,self.grid_width-4)
return y, x | [
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acutesoftware/AIKIF | aikif/toolbox/image_tools.py | resize | def resize(fname, basewidth, opFilename):
""" resize an image to basewidth """
if basewidth == 0:
basewidth = 300
img = Image.open(fname)
wpercent = (basewidth/float(img.size[0]))
hsize = int((float(img.size[1])*float(wpercent)))
img = img.resize((basewidth,hsize), Image.ANTIALIAS)
i... | python | def resize(fname, basewidth, opFilename):
""" resize an image to basewidth """
if basewidth == 0:
basewidth = 300
img = Image.open(fname)
wpercent = (basewidth/float(img.size[0]))
hsize = int((float(img.size[1])*float(wpercent)))
img = img.resize((basewidth,hsize), Image.ANTIALIAS)
i... | [
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acutesoftware/AIKIF | aikif/toolbox/image_tools.py | print_stats | def print_stats(img):
""" prints stats, remember that img should already have been loaded """
stat = ImageStat.Stat(img)
print("extrema : ", stat.extrema)
print("count : ", stat.count)
print("sum : ", stat.sum)
print("sum2 : ", stat.sum2)
print("mean : ", stat.mean... | python | def print_stats(img):
""" prints stats, remember that img should already have been loaded """
stat = ImageStat.Stat(img)
print("extrema : ", stat.extrema)
print("count : ", stat.count)
print("sum : ", stat.sum)
print("sum2 : ", stat.sum2)
print("mean : ", stat.mean... | [
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acutesoftware/AIKIF | aikif/toolbox/image_tools.py | print_all_metadata | def print_all_metadata(fname):
""" high level that prints all as long list """
print("Filename :", fname )
print("Basename :", os.path.basename(fname))
print("Path :", os.path.dirname(fname))
print("Size :", os.path.getsize(fname))
img = Image.open(fname)
# get the image's wi... | python | def print_all_metadata(fname):
""" high level that prints all as long list """
print("Filename :", fname )
print("Basename :", os.path.basename(fname))
print("Path :", os.path.dirname(fname))
print("Size :", os.path.getsize(fname))
img = Image.open(fname)
# get the image's wi... | [
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acutesoftware/AIKIF | aikif/toolbox/image_tools.py | get_metadata_as_dict | def get_metadata_as_dict(fname):
""" Gets all metadata and puts into dictionary """
imgdict = {}
try:
imgdict['filename'] = fname
imgdict['size'] = str(os.path.getsize(fname))
imgdict['basename'] = os.path.basename(fname)
imgdict['path'] = os.path.dirname(fname)
img ... | python | def get_metadata_as_dict(fname):
""" Gets all metadata and puts into dictionary """
imgdict = {}
try:
imgdict['filename'] = fname
imgdict['size'] = str(os.path.getsize(fname))
imgdict['basename'] = os.path.basename(fname)
imgdict['path'] = os.path.dirname(fname)
img ... | [
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acutesoftware/AIKIF | aikif/toolbox/image_tools.py | get_metadata_as_csv | def get_metadata_as_csv(fname):
""" Gets all metadata and puts into CSV format """
q = chr(34)
d = ","
res = q + fname + q + d
res = res + q + os.path.basename(fname) + q + d
res = res + q + os.path.dirname(fname) + q + d
try:
res = res + q + str(os.path.getsize(fname)) + q + d
... | python | def get_metadata_as_csv(fname):
""" Gets all metadata and puts into CSV format """
q = chr(34)
d = ","
res = q + fname + q + d
res = res + q + os.path.basename(fname) + q + d
res = res + q + os.path.dirname(fname) + q + d
try:
res = res + q + str(os.path.getsize(fname)) + q + d
... | [
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