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write_3dmorph_settings.py
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write_3dmorph_settings.py
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import os
output_directory = ''
threemorph_run_name = ''
output_directory += os.sep+threedmorph_run_name
install_dir = '/home/geo/hull/ph269/software/AutoMorph'
l = open('dirs_focused.txt','r')
out_dir_list = []
for line in l:
directory = line.strip()
sampleID = os.path.basename(directory)
sample_out_directory = output_directory+os.sep+sampleID
segmented_directory = directory
focused_directory = directory+'/final/focused_unlabeled'
print "in: "+segmented_directory
print "out: "+sample_out_directory
if os.path.exists(focused_directory):
out_dir_list.append(sample_out_directory)
if not os.path.exists(sample_out_directory):
os.makedirs(sample_out_directory)
settings_text = []
settings_text.append("directory = "+segmented_directory)
settings_text.append("path_run3dmorph = /home/geo/hull/ph269/software/AutoMorph/run3dmorph")
settings_text.append("path_run2dmorph = /home/geo/hull/ph269/software/AutoMorph/run2dmorph")
settings_text.append("output_dir = " + sample_out_directory)
settings_text.append("sampleID = " +sampleID)
settings_text.append("macro_mode = False")
settings_text.append("kernel_size_SF = []")
settings_text.append("fiji_architecture = 64")
settings_text.append("unit = micron")
settings_text.append("calibration = 0.975")
settings_text.append("num_slices = 25")
settings_text.append("zstep = 31.1")
settings_text.append("kernel_size_OF = 105")
settings_text.append("downsample_grid_size = 1")
settings_text.append("savePDF = []")
settings_text.append("intensity_range_in = []")
settings_text.append("intensity_range_out = []")
settings_text.append("gamma = []")
settings_text.append("threshold_adjustment = []")
settings_text.append("noise_limit = []")
settings_text.append("geom3d_path = /home/geo/hull/ph269/software/AutoMorph/run3dmorph/src/geom3d-2014.10.13/geom3d/meshes3d")
settings_text.append("mbb_path = /home/geo/hull/ph269/software/AutoMorph/run3dmorph/src")
settings_text.append("mesh2pdf_path = /home/geo/hull/ph269/software/AutoMorph/run3dmorph/src/mesh2pdf")
settings_text.append("media9_path = /home/geo/hull/ph269/software/AutoMorph/run3dmorph/src")
settings_text.append("run_latex = true")
# print settings_text
f = open(sample_out_directory+os.sep+'3dmorph_settings.txt', 'w')
for setting in settings_text:
f.write(setting+'\n')
f.close()
else:
print "no focused_unlabeled directory: "+directory
# Write directory list
f = open('dirs_'+threedmorph_run_name+'.txt', 'w')
for directory in out_dir_list:
f.write(directory+'\n')
f.close()