self.bin_opts = opts
def process(self):
self.fout = self.get_tmp_file(suffix = ".mrc")
self.flog = self.get_tmp_file(suffix = ".log")
## ndsafir is a bit weird about where it prints log. The actual log
## is being printed to stderr. Then, it appears it has a bug which
## causes the sampling value to be printed to stdout during the first
## iteration. We throw this away by redirecting stdout to devnull.
with open(os.devnull, "w") as null:
super(ndsafir, self).process(
[self.bin, self.fin.name, self.fout.name ] + self.bin_opts,
stderr = self.flog,
stdout = null,
)
def send_child(self):
self.basename = os.path.splitext(self.parent.getName())[0]
self.child_name = self.basename + "_DN.mrc"
super(ndsafir, self).send_child()
if __name__ == "__main__":
chain = omero_scripts_processing.chain([
ndsafir(bin_path = "/usr/local/priism/bin/ndsafir_priism")
])
chain.launch()
self.code = self.protect_exit(self.code)
def run_matlab(self):
## 10min should be enough
super(fastSPDM, self).run_matlab(timeout=10)
def send_child(self):
child_sufix = "_imstres_pz_%i.tif" % self.options["pxsz"]
fout_name = os.path.splitext(self.fin.name)[0] + child_sufix
## FIXME we should not have to actually open a file
self.fout = open(fout_name, "r")
self.basename = os.path.splitext(self.parent.getName())[0]
self.child_name = self.basename + child_sufix
super(fastSPDM, self).send_child()
## Because this was not created as temporary file...
self.fout.close()
try:
os.unlink(fout_name)
except OSError as e:
if e.errno != errno.ENOENT: # No such file or directory
raise
if __name__ == "__main__":
chain = omero_scripts_processing.chain([fastSPDM()])
chain.launch()