def dump_frames(args, v_info):
if args.frame_rate is None:
frame_rate = v_info["frame_rate"]
else:
frame_rate = args.frame_rate
cmd = [
find_executable("avconv", "ffmpeg"), "-loglevel", "info", "-r",
str(frame_rate), "-i", args.video, "-filter:v", "yadif", "-ss",
str(args.offset), "-t",
str(args.duration)
]
if args.width != 0:
if v_info["dar"] is not None:
src_width, src_height = v_info["dar"].split(":")
else:
src_width, src_height = map(v_info.get, ["width", "height"])
src_width, src_height = map(int, [src_width, src_height])
width = args.width
height = (args.width * src_height) / src_width
cmd += ["-s", "{}x{}".format(width, height)]
cmd += ["{}/%05d.png".format(args.dist)]
print("exec: {}".format(" ".join(cmd)))
subprocess.check_call(cmd)
def open_dir(directory):
cmd = [
find_executable("xdg-open", "open"),
directory
]
print("exec: {}".format(" ".join(cmd)))
subprocess.check_call(cmd, stderr=subprocess.PIPE)
def get_video_info(video):
cmd = [
find_executable("avprobe", "ffprobe"), "-loglevel", "error",
"-show_streams", "-show_format_entry", "width", "-show_format_entry",
"height", "-show_format_entry", "display_aspect_ratio",
"-show_format_entry", "avg_frame_rate", video
]
print("exec: {}".format(" ".join(cmd)))
out = subprocess.check_output(cmd, stderr=subprocess.PIPE)
info = {}
for line in out.split(os.linesep):
kv = line.split("=")
if len(kv) == 1:
k = kv[0]
v = None
elif len(kv) == 2:
k, v = kv
else:
raise "Invalid line format: {}".format(kv)
if k not in info:
info[k] = v
info["dar"] = info.get("display_aspect_ratio")
info["frame_rate"] = parse_frame_rate(info.get("avg_frame_rate"))
return info
def get_video_info(video):
cmd = [
find_executable("avprobe", "ffprobe"),
"-loglevel", "error",
"-show_streams",
"-show_format_entry", "width",
"-show_format_entry", "height",
"-show_format_entry", "display_aspect_ratio",
"-show_format_entry", "avg_frame_rate",
video
]
print("exec: {}".format(" ".join(cmd)))
out = subprocess.check_output(cmd, stderr=subprocess.PIPE)
info = {}
for line in out.split(os.linesep):
kv = line.split("=")
if len(kv) == 1:
k = kv[0]
v = None
elif len(kv) == 2:
k, v = kv
else:
raise "Invalid line format: {}".format(kv)
if k not in info:
info[k] = v
info["dar"] = info.get("display_aspect_ratio")
info["frame_rate"] = parse_frame_rate(info.get("avg_frame_rate"))
return info
def dump_frames(args, v_info):
if args.frame_rate is None:
frame_rate = v_info["frame_rate"]
else:
frame_rate = args.frame_rate
cmd = [
find_executable("avconv", "ffmpeg"),
"-loglevel", "info",
"-r", str(frame_rate),
"-i", args.video,
"-filter:v", "yadif",
"-ss", str(args.offset),
"-t", str(args.duration)
]
if args.width != 0:
if v_info["dar"] is not None:
src_width, src_height = v_info["dar"].split(":")
else:
src_width, src_height = map(v_info.get, ["width", "height"])
src_width, src_height = map(int, [src_width, src_height])
width = args.width
height = (args.width * src_height) / src_width
cmd += ["-s", "{}x{}".format(width, height)]
cmd += ["{}/%05d.png".format(args.dist)]
print("exec: {}".format(" ".join(cmd)))
subprocess.check_call(cmd)
def open_gif(gif):
cmd = [
find_executable("xdg-open", "open"),
gif
]
print("exec: {}".format(" ".join(cmd)))
subprocess.check_call(cmd, stderr=subprocess.PIPE)
def get_video_info(video):
cmd = [
find_executable("avprobe", "ffprobe"),
"-of", "json",
"-loglevel", "error",
"-show_streams",
video
]
print("exec: {}".format(" ".join(cmd)))
out = subprocess.check_output(cmd, stderr=subprocess.PIPE)
out = json.loads(out)
for stream in out["streams"]:
if stream["codec_type"] != "video":
continue
info = stream
info["dar"] = info.get("display_aspect_ratio")
info["frame_rate"] = parse_frame_rate(info.get("avg_frame_rate"))
return info
def open_dir(directory):
cmd = [find_executable("xdg-open", "open"), directory]
print("exec: {}".format(" ".join(cmd)))
subprocess.check_call(cmd, stderr=subprocess.PIPE)
import util
import sys
import os
import re
inkscape = util.find_executable("inkscape", ["/Applications/Inkscape.app/Contents/Resources/bin/inkscape", "/usr/bin/inkscape"])
def svg2eps(svg_fname, eps_fname):
os.popen(inkscape + " " + svg_fname + " --export-eps=" + eps_fname)
def svg2png(svg_fname, png_fname, width="500"):
os.popen(inkscape + " " + svg_fname + " --export-png=" + png_fname + " --export-width=" + width)
def svg2pdf(svg_fname, pdf_fname):
os.popen(inkscape + " " + svg_fname + " --export-pdf=" + pdf_fname)
## MAIN
if (len(sys.argv) < 2):
raise Exception("Syntax: batch_svg2image <path> <output format>")
for fname in os.listdir(sys.argv[1]):
if (fname[len(fname)-4:] == ".svg"):
base_fname = sys.argv[1] + "/" + fname[0:len(fname)-4]
print "converting", base_fname
if (len(sys.argv) < 3 or sys.argv[2] == "png"):
svg2png(base_fname + ".svg", base_fname + ".png")
elif (sys.argv[2] == "eps"):
svg2eps(base_fname + ".svg", base_fname + ".eps")
elif (sys.argv[2] == "pdf"):
svg2pdf(base_fname + ".svg", base_fname + ".pdf")
else:
raise Exception("unknown output figure format: " + sys.argv[2])
import util
import sys
import os
import re
inkscape = util.find_executable("inkscape", [
"/Applications/Inkscape.app/Contents/Resources/bin/inkscape",
"/usr/bin/inkscape"
])
def svg2eps(svg_fname, eps_fname):
os.popen(inkscape + " " + svg_fname + " --export-eps=" + eps_fname)
def svg2png(svg_fname, png_fname, width="500"):
os.popen(inkscape + " " + svg_fname + " --export-png=" + png_fname +
" --export-width=" + width)
def svg2pdf(svg_fname, pdf_fname):
os.popen(inkscape + " " + svg_fname + " --export-pdf=" + pdf_fname)
## MAIN
if (len(sys.argv) < 2):
raise Exception("Syntax: batch_svg2image <path> <output format>")
for fname in os.listdir(sys.argv[1]):
if (fname[len(fname) - 4:] == ".svg"):
base_fname = sys.argv[1] + "/" + fname[0:len(fname) - 4]
#!/usr/bin/python
import os
from chemistry import ChemGraph
from chemconstants import *
import util
import svg
import sys
molconvert = util.find_executable("molconvert", ["/Applications/MarvinBeans/bin/molconvert", "/home/eladn/ChemAxon/MarvinBeans/bin/molconvert"])
inkscape = util.find_executable("inkscape", ["/Applications/Inkscape.app/Contents/Resources/bin/inkscape", "/usr/bin/inkscape"])
import gzip
global map_compound2graph; map_compound2graph = {}
global map_hash2compound; map_hash2compound = {}
global map_hash2compound_unchiral; map_hash2compound_unchiral = {}
def load_mcard(filename, gzipped=False):
if (gzipped):
file = gzip.GzipFile(filename, 'r')
else:
file = open(filename, 'r')
print >> sys.stderr, "Parsing database file: %s" % filename
# Parse the Mcard SDF database file:
while True:
header = file.readline()
if (header == ""):
break
body = util.readlines_until_mark(file, "$$$$")
#!/usr/bin/python
import os
from chemistry import ChemGraph
from chemconstants import *
import util
import svg
import sys
molconvert = util.find_executable("molconvert", [
"/Applications/MarvinBeans/bin/molconvert",
"/home/eladn/ChemAxon/MarvinBeans/bin/molconvert"
])
inkscape = util.find_executable("inkscape", [
"/Applications/Inkscape.app/Contents/Resources/bin/inkscape",
"/usr/bin/inkscape"
])
import gzip
global map_compound2graph
map_compound2graph = {}
global map_hash2compound
map_hash2compound = {}
global map_hash2compound_unchiral
map_hash2compound_unchiral = {}
def load_mcard(filename, gzipped=False):
if (gzipped):
file = gzip.GzipFile(filename, 'r')
else:
def open_gif(gif):
cmd = [find_executable("xdg-open", "open"), gif]
print("exec: {}".format(" ".join(cmd)))
subprocess.check_call(cmd, stderr=subprocess.PIPE)
