def cli(filename, f_min, f_max, output,
quality_factor, spring_constant, resonance_frequency, temperature):
# This function needs to be broken up into component pieces.
# For example, the reproduce python, reproduce cli bits can easily be their
# own functions (and in fact, may make more sense as __repr__ methods of
# classes)
# The report generator should also be its own function.
if resonance_frequency is None:
resonance_frequency = (f_min + f_max) / 2.0
file_path = os.path.abspath(filename)
with h5py.File(filename, 'r') as f:
date = f.attrs['date']
time = f.attrs['time'].replace(':', '')
if output is None:
cli_reproduce = """calck "{file_path}" {f_min} {f_max} -Q {Q} -k {k} -f {f} -T {T}""".format(file_path=file_path, f_min=f_min, f_max=f_max, Q=quality_factor,
k=spring_constant, f=resonance_frequency, T=temperature)
else:
cli_reproduce = """calck "{file_path}" {f_min} {f_max} -o {output} -Q {Q} -k {k} -f {f} -T {T}""".format(file_path=file_path, f_min=f_min, f_max=f_max, Q=quality_factor,
k=spring_constant, f=resonance_frequency, T=temperature, output=output)
python_reproduce = """\
import brownian._calck
bmf = brownian._calck.calck("{file_path}",
f_min={f_min}, f_max={f_max},
quality_factor={Q},
spring_constant={k},
resonance_frequency={f},
temperature={T})
print(bmf.report())
""".format(file_path=file_path, f_min=f_min, f_max=f_max, Q=quality_factor,
k=spring_constant, f=resonance_frequency, T=temperature)
bmf = calck(filename, f_min, f_max,
quality_factor, spring_constant, resonance_frequency, temperature)
if output is None:
text = u"""\
Generated by brownian version {version}.
Reproduce this analysis with the following shell command:
{cli_reproduce}
or with the following python code:
{python_reproduce}
{report}
""".format(cli_reproduce=cli_reproduce,
python_reproduce=python_reproduce, report = bmf.rst_report(),
version=brownian.__version__)
click.echo(text)
return 0
else:
files = Bunch(fit="fit.png", reduced_residuals="reduced_residuals.png",
cdf='cdf.png')
bmf.plot_fit(files.fit)
bmf.plot_reduced_residuals(files.reduced_residuals)
bmf.plot_cdf(files.cdf)
ReST = u"""\
Report
======
{report}
.. image:: {files.fit}
.. image:: {files.reduced_residuals}
.. image:: {files.cdf}
Reproduce this analysis with the following shell command:
.. code:: bash
{cli_reproduce}
or with the following python code:
.. code:: python
{python_reproduce}
Generated by ``brownian`` version ``{version}``.
""".format(files=files, cli_reproduce=cli_reproduce,
python_reproduce=python_reproduce, report = bmf.rst_report(),
version=brownian.__version__)
ext = file_extension(output)
if ext not in ('zip', 'html'):
click.echo('output file extension must be zip or html, not {0}'.format(ext))
return -1
elif ext == 'html':
image_dependent_html = docutils.core.publish_string(ReST, writer_name='html')
self_contained_html = unicode(img2uri(image_dependent_html), 'utf8')
# io module instead of built-in open because it allows specifying
# encoding. See http://stackoverflow.com/a/22288895/2823213
with io.open(output, 'w', encoding='utf8') as f:
f.write(self_contained_html)
for filename in files.values():
silentremove(filename)
return 0
elif ext == 'zip':
files.html = date+'-'+time+'.html'
files.rst = date+'-'+time+'.rst'
image_dependent_html = unicode(
docutils.core.publish_string(ReST, writer_name='html'), 'utf8'
)
with io.open(files.html, 'w', encoding='utf8') as f:
f.write(image_dependent_html)
with io.open(files.rst, 'w', encoding='utf8') as f:
f.write(ReST)
with zipfile.ZipFile(output, 'w') as z:
for f in files.values():
z.write(f)
# Delete non-zipped version of the files
for f in files.values():
silentremove(f)
return 0
def tearDown(self):
silentremove(self.testv1)
silentremove(self.testv2)
silentremove(self.converted)
def tearDown(self):
self.fh.close()
silentremove(self.filename)
