def __init__(self, src_zip_file, dst_zip_file):
self.color_aliases = {}
self.region_color_defaults = {}
self.currentplyscope = None
self.global_options = {
#MeshGenerationOptions.minimum_diameter: 1.0
}
self.src_zip_file = src_zip_file
self.dst_zip_file = dst_zip_file
self.op_files = []
self.op_dir = '/tmp/mf/meshbuilder/'
LocMgr.ensure_dir_exists(self.op_dir)
def __init__(self, src_zip_file, dst_zip_file):
self.color_aliases = {}
self.region_color_defaults = {}
self.currentplyscope = None
self.global_options = {
#MeshGenerationOptions.minimum_diameter: 1.0
}
self.src_zip_file = src_zip_file
self.dst_zip_file = dst_zip_file
self.op_files = []
self.op_dir = '/tmp/mf/meshbuilder/'
LocMgr.ensure_dir_exists(self.op_dir)
def testComparisonFailureTransplantingALeafNode(self):
"""Remap each leaf node in a complex swc file, onto
different internal nodes of the morphology,
and check that the morphology is considered different
"""
testSrcsPath = LocMgr().get_test_srcs_path()
srcSWCFile = Join(testSrcsPath, "swc_srcs/28o_spindle20aFI.CNG.swc")
m = MorphologyArray.fromSWC(srcSWCFile)
# Find the leaf nodes:
leaf_nodes = m.get_leaf_vertices_indices()
for new_parent in [0, 10, 20, leaf_nodes[-1]]:
for l in leaf_nodes[:-1]:
v = m._vertices.copy()
c = m._connectivity.copy()
# Rewrite the connectivity matrix, mapping the
# leaf to a new_parent:
c[c == l] = new_parent
mNew = MorphologyArray(vertices=v, connectivity=c)
assert not MorphArrayComparison.are_same(
m, mNew, max_node_distance=0.00001)
def testComparisonFailureAddingEpsilon2(self):
"""Load and complex .swc file, and
change each [x, y, z, r] value in the vertices matrix
individually, to check that it is not the same.
"""
testSrcsPath = LocMgr().get_test_srcs_path()
srcSWCFile = Join(testSrcsPath, "swc_srcs/28o_spindle20aFI.CNG.swc")
m = MorphologyArray.fromSWC(srcSWCFile)
MFRandom.seed(0)
for i in range(len(m)):
print i, len(m)
for j in range(4):
# Only test 2% of cases:
if not np.random.rand() < 0.02:
continue
m1 = MorphologyArray.fromSWC(srcSWCFile)
m1._vertices[i, j] = m1._vertices[i, j] + 0.01
assert MorphArrayComparison.are_same(m,
m1,
max_node_distance=0.02)
assert not MorphArrayComparison.are_same(
m, m1, max_node_distance=0.005)
def config(cls):
from morphforge.core.mgrs.locmgr import LocMgr
if cls._initialised_state == LogMgrState.Configuring:
return
if cls._initialised_state == LogMgrState.Ready:
return
cls._initialised_state = LogMgrState.Configuring
logfilename = os.path.join(LocMgr.get_log_path(), 'log.html')
logging.basicConfig(filename=logfilename, level=logging.INFO)
cls._initialised_state = LogMgrState.Ready
cls.info_from_logger('Logger Started OK')
import subprocess
import glob
import re
import itertools
from glob import glob as Glob
from os.path import join as Join
from Cheetah.Template import Template
import mreorg
from morphforge.core.mgrs.locmgr import LocMgr
root = os.path.normpath( os.path.join( LocMgr.get_root_path(), "..") )
examples_src_dir = os.path.join(root, "src/morphforgeexamples/")
#"/home/michael/hw/morphforge/doc"
doc_src_dir = os.path.normpath( os.path.join(root, "doc") )
examples_dst_dir = os.path.join(root, "doc/srcs_generated_examples")
examples_dst_dir_images = os.path.join(root, "doc/srcs_generated_examples/images/")
examples_build_dir = os.path.join( LocMgr.get_tmp_path(), "mf_doc_build")
examples_build_dir_image_out = os.path.join( examples_build_dir, "images/")
dirs = ['morphology', 'singlecell_simulation', 'multicell_simulation', 'advanced_examples']#, 'assorted' ]
example_subdirs = [ d for d in os.listdir(examples_src_dir) if d.startswith("""exset""") ]
def parse_tagselector_string(s):
if not _ParseCache.lex:
_ParseCache.lex = ply.lex.lex()
if not _ParseCache.yacc:
_ParseCache.yacc = ply.yacc.yacc(tabmodule='tagselectorparser_parsetab', outputdir=LocMgr.ensure_dir_exists('/tmp/parsetabs/'), debug=0, write_tables=1, optimize=1)
return _ParseCache.yacc.parse(s, lexer=_ParseCache.lex.clone())