示例#1
0
def install_make():
    click.secho("We need to install make ...\n", fg="red")
    if platform.system() != "Windows":
        call_cmd("sudo -k -H apt install make")
    else:
        click.fail("As a windows user, you must install `make` manually. "
                   "See: http://bfy.tw/NI8r")
示例#2
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def cli(ctx):
    """
    Interface with a YubiKey via the command line.
    """
    subcmd = next(c for c in COMMANDS if c.name == ctx.invoked_subcommand)
    transports = getattr(subcmd, 'transports', TRANSPORT.usb_transports())
    if transports:
        try:
            descriptors = list(get_descriptors())
        except usb.core.NoBackendError:
            click.fail('No PyUSB backend detected!')
        n_keys = len(descriptors)
        if n_keys == 0:
            ctx.fail('No YubiKey detected!')
        if n_keys > 1:
            ctx.fail('Multiple YubiKeys detected. Only a single YubiKey at a '
                     'time is supported.')
        descriptor = descriptors[0]
        if descriptor.mode.transports & transports:
            try:
                ctx.obj['dev'] = descriptor.open_device(transports)
                if not ctx.obj['dev']:  # Key should be there, busy?
                    raise FailedOpeningDeviceException()
            except FailedOpeningDeviceException:
                ctx.fail('Failed connecting to the YubiKey. Is it in use by '
                         'another process?')
        else:
            req = ', '.join((t.name for t in TRANSPORT if t & transports))
            click.echo("Command '{}' requires one of the following transports "
                       "to be enabled: '{}'.".format(subcmd.name, req))
            ctx.fail("Use 'ykman mode' to set the enabled connections.")
示例#3
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    def create_api_key():
        """ Interactively create a new API key via Zotero's OAuth API.

        Requires the user to enter a verification key displayed in the browser.

        :returns:   API key and the user's library ID
        """
        auth = OAuth1Service(
            name='zotero',
            consumer_key=CLIENT_KEY,
            consumer_secret=CLIENT_SECRET,
            request_token_url=REQUEST_TOKEN_URL,
            access_token_url=ACCESS_TOKEN_URL,
            authorize_url=AUTH_URL,
            base_url=BASE_URL)
        token, secret = auth.get_request_token(
            params={'oauth_callback': 'oob'})
        auth_url = auth.get_authorize_url(token)
        auth_url += '&' + urlencode({
            'name': 'zotero-cli',
            'library_access': 1,
            'notes_access': 1,
            'write_access': 1,
            'all_groups': 'read'})
        click.echo("Opening {} in browser, please confirm.".format(auth_url))
        click.launch(auth_url)
        verification = click.prompt("Enter verification code")
        token_resp = auth.get_raw_access_token(
            token, secret, method='POST',
            data={'oauth_verifier': verification})
        if not token_resp:
            logging.debug(token_resp.content)
            click.fail("Error during API key generation.")
        access = urlparse.parse_qs(token_resp.text)
        return access['oauth_token'][0], access['userID'][0]
示例#4
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    def create_api_key():
        """ Interactively create a new API key via Zotero's OAuth API.

        Requires the user to enter a verification key displayed in the browser.

        :returns:   API key and the user's library ID
        """
        auth = OAuth1Service(
            name='zotero',
            consumer_key=CLIENT_KEY,
            consumer_secret=CLIENT_SECRET,
            request_token_url=REQUEST_TOKEN_URL,
            access_token_url=ACCESS_TOKEN_URL,
            authorize_url=AUTH_URL,
            base_url=BASE_URL)
        token, secret = auth.get_request_token(
            params={'oauth_callback': 'oob'})
        auth_url = auth.get_authorize_url(token)
        auth_url += '&' + urlencode({
            'name': 'zotero-cli',
            'library_access': 1,
            'notes_access': 1,
            'write_access': 1,
            'all_groups': 'read'})
        click.echo("Opening {} in browser, please confirm.".format(auth_url))
        click.launch(auth_url)
        verification = click.prompt("Enter verification code")
        token_resp = auth.get_raw_access_token(
            token, secret, method='POST',
            data={'oauth_verifier': verification})
        if not token_resp:
            logging.debug(token_resp.content)
            click.fail("Error during API key generation.")
        access = urlparse.parse_qs(token_resp.text)
        return access['oauth_token'][0], access['userID'][0]
示例#5
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def state(ctx, module, identifier, db, table, key_map, verbose, namespace):
    """
    Dump the current state of the identifier for the specified module from Redis DB or CONFIG_FILE
    """
    if not multi_asic.is_multi_asic() and namespace != DEFAULT_NAMESPACE:
        click.echo("Namespace option is not valid for a single-ASIC device")
        ctx.exit()

    if multi_asic.is_multi_asic() and (namespace != DEFAULT_NAMESPACE
                                       and namespace
                                       not in multi_asic.get_namespace_list()):
        click.echo("Namespace option is not valid. Choose one of {}".format(
            multi_asic.get_namespace_list()))
        ctx.exit()

    if module not in plugins.dump_modules:
        click.echo("No Matching Plugin has been Implemented")
        ctx.exit()

    if verbose:
        os.environ["VERBOSE"] = "1"
    else:
        os.environ["VERBOSE"] = "0"

    ctx.module = module
    obj = plugins.dump_modules[module]()

    if identifier == "all":
        ids = obj.get_all_args(namespace)
    else:
        ids = identifier.split(",")

    params = {}
    collected_info = {}
    params['namespace'] = namespace
    for arg in ids:
        params[plugins.dump_modules[module].ARG_NAME] = arg
        try:
            collected_info[arg] = obj.execute(params)
        except ValueError as err:
            click.fail(f"Failed to execute plugin: {err}")

    if len(db) > 0:
        collected_info = filter_out_dbs(db, collected_info)

    vidtorid = extract_rid(collected_info, namespace)

    if not key_map:
        collected_info = populate_fv(collected_info, module, namespace)

    for id in vidtorid.keys():
        collected_info[id]["ASIC_DB"]["vidtorid"] = vidtorid[id]

    print_dump(collected_info, table, module, identifier, key_map)

    return
示例#6
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def get_confluence_cmd():
    """Assemble mandatory parameters for the Confluence command."""
    try:
        command_path = environ['CONFLUENCE_COMMAND_PATH']
    except KeyError as error:
        click.fail('Unable to access {}'.format(str(error)))

    credentials = get_credentials()
    return [
        command_path, '--server', CONFLUENCE_URL, '--user',
        credentials['username'], '--password', credentials['password']
    ]
示例#7
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def growth(ctx, **kwargs):
    """Attempts to compute growth rate (i.e. fit e^(2x)) from DynVector
    data, typically an integrated quantity like electric or magnetic
    field energy.
    """
    vlog(ctx, 'Starting growth')
    pushChain( ctx, 'growth', **kwargs) 
    data = ctx.obj['data']
    
    for dat in data.iterator(kwargs['use']):
        time = dat.getGrid()
        values = dat.getValues()
        numDims = dat.getNumDims()
        if numDims > 1:
            click.fail(click.style("'growth' is available only for 1D data (used on {:d}D data)".format(numDims), fg='red'))
        #end
        
        bestParams, bestR2, bestN = fitGrowth(time[0], values[..., 0],
                                              minN=kwargs['minn'],
                                              maxN=kwargs['maxn'],
                                              p0=kwargs['guess'])

        if kwargs['plot'] is True:
            vlog(ctx, 'growth: Plotting data and fit')
            plt.style.use(os.path.dirname(os.path.realpath(__file__)) \
                      + "/../output/postgkyl.mplstyle")
            fig, ax = plt.subplots()
            ax.plot(time[0], values[..., 0], '.')
            ax.set_autoscale_on(False)
            ax.plot(time[0], exp2(time[0], *bestParams))
            ax.grid(True)
            plt.show()
        #end

        if kwargs['instantaneous'] is True:
            vlog(ctx, 'growth: Plotting instantaneous growth rate')
            gammas = []
            for i in range(1,len(time[0])-1):
                gamma = (values[i+1,0] - values[i-1,0])/(2*values[i,0]*(time[0][i+1] - time[0][i-1]))
                gammas.append(gamma)
            
            plt.style.use(os.path.dirname(os.path.realpath(__file__)) \
                      + "/../output/postgkyl.mplstyle")
            fig, ax = plt.subplots()
            ax.plot(time[0][1:-1], gammas)
            #ax.set_autoscale_on(False)
            ax.grid(True)
            plt.show()
        #end
    #end
    vlog(ctx, 'Finishing growth')
示例#8
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文件: cli.py 项目: kfdm/alfred-cli
def import_(bundleid):
    for path, plist in alfredcli.util.workflows():
        if plist.get("bundleid") == bundleid:
            break
    else:
        click.fail("Unable to find bundle id: {0}".format(bundleid))

    source_dir = os.path.dirname(path)
    dest_dir = os.getcwd()
    click.echo("Importing {0} from {1} to {2}".format(bundleid, source_dir, dest_dir))

    for root, dirs, files in os.walk(source_dir):
        for f in files:
            # if f != 'info.plist':
            #   continue
            source_path = os.path.join(root, f)
            dest_path = os.path.join(dest_dir, f)
            click.echo("Copying {0} to {1}".format(source_path, dest_path))
            shutil.copy(source_path, dest_path)
示例#9
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文件: cli.py 项目: zuxfoucault/pypes
def motion(input: hansel.Crumb, extra: pd.DataFrame, out_file: hansel.Crumb):
    """ Create in `out_path` an Excel spreadsheet with some of the motion statistics obtained from the
    `statistics_files` output of the nipype.RapidArt found in the hansel.Crumb `motion_file_cr`.

    Examples: \n
    nitap motion -i "/data/hansel/cobre/{sid}/{session}/rest/artifact_stats/motion_stats.json" -o motion.xls\n
    nitap motion -i "/data/nuk/out/{group}/{sid}/session_0/rest/artifact_stats/motion_stats.json" -o motion.xls\n
    """
    from neuro_pypes.fmri.utils import motion_stats_sheet

    crumb_args = list(input.open_args())
    df = motion_stats_sheet(input, crumb_args)

    if extra:
        extra_columns = set(extra.columns.values)
        matched_args = extra_columns.intersection(crumb_args)
        if not matched_args:
            click.fail('Found no matches in the spreadsheet file between: '
                       '"{}" and "{}".'.format(extra_columns, crumb_args))
        df.join(extra, on=matched_args)

    df.to_excel(out_file)
    print(
        'Successfully wrote the motions spreadsheet in "{}".'.format(out_file))
示例#10
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def main(group_id, location, time_boundary, event_status, pandoc, force):
    key_path = os.path.normpath(os.path.expanduser('~/.meetup.com-key'))
    if os.path.exists(key_path):
        with io.open(key_path, encoding='utf8') as fh:
            key = fh.read().strip()
    else:
        key = None
    cache = FileCache('.web_cache', forever=True)
    requests = CacheControl(Session(),
                            cache,
                            cache_etags=False,
                            heuristic=ExpiresAfter(days=1))

    while True:
        resp = requests.get('https://api.meetup.com/status',
                            params=dict(key=key))
        if resp.status_code == 200 and resp.json().get('status') == 'ok':
            break
        elif resp.status_code == 200 and any(
                'auth_fail' == e.code for e in resp.json().get('errors', [])):
            click.echo(
                'Your meetup.com key is required. You can get it from https://secure.meetup.com/meetup_api/key/\n'
            )

            if click.confirm(
                    'Open https://secure.meetup.com/meetup_api/key/ in your web browser?'
            ):
                click.launch('https://secure.meetup.com/meetup_api/key/')

            click.echo('')
            key = click.prompt('Key', hide_input=True)
        else:
            raise click.ClickException(
                'Failed to get meetup.com status. Response was {!r} {!r}'.
                format(resp.status_code, resp.text))

    click.secho(
        'For convenience your key is saved in `{}`.\n'.format(key_path),
        fg='magenta')
    with open(key_path, 'w') as fh:
        fh.write(key)

    while not location:
        location = location or get_input(
            u'Location: ',
            completer=WordCompleter(
                [u'cluj', u'iasi', u'timisoara', u'bucuresti'],
                ignore_case=True))

    while True:
        group_id = group_id or get_input(
            u'Group ID: ',
            completer=WordCompleter([
                u'RoPython-Bucuresti', u'RoPython-Cluj', u'RoPython_Iasi',
                u'RoPython-Timisoara'
            ],
                                    ignore_case=True))

        resp = requests.get('https://api.meetup.com/2/events',
                            params=dict(
                                key=key,
                                group_urlname=group_id,
                                time=time_boundary,
                                status=event_status,
                            ))
        if resp.status_code == 200:
            json = resp.json()
            if json['results']:
                break
            else:
                click.secho(
                    'Invalid group `{}`. It has no events!'.format(group_id),
                    fg='red')
                group_id = None
        if resp.status_code == '400':
            click.fail(
                'Failed to get make correct request. Response was {!r}'.format(
                    resp.text))
        else:
            click.secho('Invalid group `{}`. Response was [{}] {!r}'.format(
                group_id, resp.status_code, resp.text),
                        fg='red')

    # click.echo(pformat(dict(resp.headers)))

    for event in json['results']:
        dt = datetime.fromtimestamp(event['time'] / 1000)
        event['duration'] = format_duration(
            event.get('duration', 3600000) / 1000)
        event['time'] = dt.strftime('%Y-%m-%d %H:%M')
        if 'how_to_find_us' in event:
            address = event['how_to_find_us'],
        else:
            address = ()
        if 'venue' in event:
            address_1 = event['venue'].get('address_1')
            if address_1:
                address += address_1,
            event['venue']['address_1'] = ', '.join(address)
        else:
            event['venue'] = {'address_1': address}
        click.echo("{time}: {name}".format(**event))
        click.echo("\t{}".format(pformat(event)))
        existing_path = glob(
            os.path.join('content', '*', dt.strftime('%Y-%m-%d*'),
                         'index.rst'))
        if existing_path and not force:
            if len(existing_path) > 1:
                click.secho('\tERROR: multiple paths matched: {}'.format(
                    existing_path))
            else:
                click.secho('\t`{}` already exists. Not importing.'.format(
                    *existing_path),
                            fg='yellow')
        else:
            target_dir = os.path.join(
                'content', location, '{}-{}'.format(dt.strftime('%Y-%m-%d'),
                                                    slugify(event['name'])))
            target_path = os.path.join(target_dir, 'index.rst')
            if not os.path.exists(target_dir):
                os.makedirs(target_dir)

            if pandoc:
                with tempfile.NamedTemporaryFile(delete=False) as fh:
                    fh.write(event['description'].encode('utf-8'))
                rst = subprocess.check_output(
                    ['pandoc', '--from=html', '--to=rst',
                     fh.name]).decode('utf-8')
                os.unlink(fh.name)
            else:
                rst = html2rest(event['description'])

            doc = u'''{name}
###############################################################

:tags: prezentari
:registration:
    meetup.com: {event_url}
:start: {time}
:duration: {duration}
:location: {venue[address_1]}, {venue[city]}, {venue[localized_country_name]}

{rst}'''.format(rst=rst, **event)
            with io.open(target_path, 'w', encoding='utf-8') as fh:
                fh.write(doc)
            click.secho('\tWrote `{}`.'.format(target_path), fg='green')
示例#11
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def main(group_id, location, time_boundary, event_status, pandoc):
    key_path = os.path.normpath(os.path.expanduser('~/.meetup.com-key'))
    if os.path.exists(key_path):
        with open(key_path) as fh:
            key = fh.read().strip()

    cache = FileCache('.web_cache', forever=True)
    requests = CacheControl(
        Session(), cache,
        cache_etags=False,
        heuristic=ExpiresAfter(days=1)
    )

    while True:
        resp = requests.get('https://api.meetup.com/status', params=dict(key=key))
        if resp.status_code == 200:
            break
        elif resp.status_code == 401:
            click.echo('Your meetup.com key is required. You can get it from https://secure.meetup.com/meetup_api/key/\n')

            if click.confirm('Open https://secure.meetup.com/meetup_api/key/ in your web browser?'):
                click.launch('https://secure.meetup.com/meetup_api/key/')

            click.echo('')
            key = click.prompt('Key', hide_input=True)
        else:
            click.fail('Failed to get meetup.com status. Response was {!r}'.format(resp.text))

    click.secho('For convenience your key is saved in `{}`.\n'.format(key_path), fg='magenta')
    with open(key_path, 'w') as fh:
        fh.write(key)

    while not location:
        location = location or get_input('Location: ', completer=WordCompleter(['cluj', 'iasi', 'timisoara'], ignore_case=True))

    while True:
        group_id = group_id or get_input('Group ID: ', completer=WordCompleter(['Cluj-py', 'RoPython-Timisoara'], ignore_case=True))

        resp = requests.get('https://api.meetup.com/2/events', params=dict(
            key=key,
            group_urlname=group_id,
            time=time_boundary,
            status=event_status,
        ))
        if resp.status_code == 200:
            json = resp.json()
            if json['results']:
                break
            else:
                click.secho('Invalid group `{}`. It has no events!'.format(group_id), fg='red')
                group_id = None
        if resp.status_code == '400':
            click.fail('Failed to get make correct request. Response was {!r}'.format(resp.text))
        else:
            click.secho('Invalid group `{}`. Response was [{}] {!r}'.format(group_id, resp.status_code, resp.text), fg='red')

    # click.echo(pformat(dict(resp.headers)))

    for event in json['results']:
        dt = datetime.fromtimestamp(event['time']/1000)
        click.echo("{}: {}".format(
            dt.strftime('%Y-%m-%d %H:%M:%S'),
            event['name']
        ))
        existing_path = glob(os.path.join('content', '*', dt.strftime('%Y-%m-%d*'), 'index.rst'))
        if existing_path:
            if len(existing_path) > 1:
                click.secho('\tERROR: multiple paths matched: {}'.format(existing_path))
            else:
                click.secho('\t`{}` already exists. Not importing.'.format(*existing_path), fg='yellow')
        else:
            target_dir = os.path.join('content', location, '{}-{}'.format(dt.strftime('%Y-%m-%d'), slugify(event['name'])))
            target_path = os.path.join(target_dir, 'index.rst')
            if not os.path.exists(target_dir):
                os.makedirs(target_dir)

            if pandoc:
                with tempfile.NamedTemporaryFile(delete=False) as fh:
                    fh.write(event['description'].encode('utf-8'))
                rst = subprocess.check_output(['pandoc', '--from=html', '--to=rst', fh.name]).decode('utf-8')
                print fh.name
                #os.unlink(fh.name)
            else:
                stream = StringIO()
                html2rest(event['description'].encode('utf-8'), writer=stream)
                rst = stream.getvalue().decode('utf-8')

            with io.open(target_path, 'w', encoding='utf-8') as fh:
                fh.write('''{name}
###############################################################

:tags: unknown
:registration:
    meetup.com: {event_url}

{rst}'''.format(rst=rst, **event))
            click.secho('\tWrote `{}`.'.format(target_path), fg='green')
示例#12
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文件: standard.py 项目: Bonelab/Ogo
def standard(ct_file_name, rods_file_name, density_file_name, densities,
             csv_file_name):
    '''Determine the calibration equation for a standard phantom.'''
    click.echo(echo_arguments('Standard Calibration', locals()))

    # Read
    click.echo('Reading input {}'.format(ct_file_name))
    ct = sitk.ReadImage(ct_file_name)

    click.echo('Reading input {}'.format(rods_file_name))
    rods = sitk.ReadImage(rods_file_name)

    # Determine number of components
    click.echo('Determining mean intensities')
    filt = sitk.LabelStatisticsImageFilter()
    filt.Execute(ct, rods)

    n_labels = len(filt.GetLabels())
    click.echo('Found {} labels'.format(n_labels))

    if len(densities) < 2:
        click.fail('Need at least 2 samples to fit a function.'
                   ' Only found {}'.format(len(densities)))

    # Get the HU samples
    HU = []
    for label in filt.GetLabels():
        # Skip background label
        if label == 0:
            continue

        HU.append(filt.GetMean(label))

    click.echo('Fitting parameters:')
    click.echo('  Densities: {}'.format(densities))
    click.echo('  HU:        {}'.format(HU))

    # Perform calibration
    calibrator = StandardCalibration()
    calibrator.fit(HU, densities)

    click.echo('Found fit:')
    click.echo('  Slope:     {}'.format(calibrator.slope))
    click.echo('  Intercept: {}'.format(calibrator.intercept))
    click.echo('  R^2:       {}'.format(calibrator.r_value**2))

    header = [
        'CT File Name', 'Rods File Name', 'Density File Name', 'slope',
        'intercept', 'r_value', 'p_value', 'std_err'
    ]
    data = {
        'CT File Name': ct_file_name,
        'Rods File Name': rods_file_name,
        'Density File Name': density_file_name,
        'slope': round(calibrator.slope, 16),
        'intercept': round(calibrator.intercept, 16),
        'r_value': round(calibrator.r_value, 16),
        'p_value': round(calibrator.p_value, 16),
        'std_err': round(calibrator.std_err, 16)
    }

    click.echo('Writing complete results to {}'.format(csv_file_name))
    write_csv(data, csv_file_name, header)

    click.echo('Calibrating density file')
    density = calibrator.slope * sitk.Cast(ct, sitk.sitkFloat32) + \
        calibrator.intercept

    click.echo('Writing density file to {}'.format(density_file_name))
    sitk.ReadImage(density, density_file_name)
示例#13
0
文件: mindways.py 项目: Bonelab/Ogo
def mindways(ct_file_name, rods_file_name, density_file_name, csv_file_name,
             water, densities):
    '''Determine the calibration equation for a Mindways phantom.

    Water and K2HPO4 densities are taken from the QC documentation
    accompanying your specific phantom.'''
    click.echo(echo_arguments('Mindways Calibration', locals()))

    # Read
    click.echo('Reading input {}'.format(ct_file_name))
    ct = sitk.ReadImage(ct_file_name)

    click.echo('Reading input {}'.format(rods_file_name))
    rods = sitk.ReadImage(rods_file_name)

    # Determine number of components
    click.echo('Determining mean intensities')
    filt = sitk.LabelStatisticsImageFilter()
    filt.Execute(ct, rods)

    n_labels = len(filt.GetLabels())
    click.echo('Found {} labels'.format(n_labels))

    if len(water) != len(densities) or len(water) != n_labels - 1:
        click.fail(
            'Number of water, K2HPO4, and segmented labels are not the same '
            '({}, {}, and {})'.format(len(water), len(densities),
                                      n_labels - 1))

    if len(water) < 2:
        click.fail('Need at least 2 samples to fit a function.'
                   ' Only found {}'.format(len(water)))

    # Get the HU samples
    HU = []
    for label in filt.GetLabels():
        # Skip background label
        if label == 0:
            continue

        HU.append(filt.GetMean(label))

    click.echo('Fitting parameters:')
    click.echo('  Water:  {}'.format(water))
    click.echo('  K2HPO4: {}'.format(densities))
    click.echo('  HU:     {}'.format(HU))

    # Perform calibration
    calibrator = MindwaysCalibration()
    calibrator.fit(HU, densities, water)

    click.echo('Found fit:')
    click.echo('  Slope:     {}'.format(calibrator.slope))
    click.echo('  Intercept: {}'.format(calibrator.intercept))
    click.echo('  R^2:       {}'.format(calibrator.r_value**2))

    header = [
        'CT File Name', 'Rods File Name', 'Density File Name', 'sigma_ref',
        'beta_ref', 'sigma_ct', 'beta_ct', 'slope', 'intercept', 'r_value',
        'p_value', 'std_err'
    ]
    data = {
        'CT File Name': ct_file_name,
        'Rods File Name': rods_file_name,
        'Density File Name': density_file_name,
        'sigma_ref': round(calibrator.sigma_ref, 16),
        'beta_ref': round(calibrator.beta_ref, 16),
        'sigma_ct': round(calibrator.sigma_ct, 16),
        'beta_ct': round(calibrator.beta_ct, 16),
        'slope': round(calibrator.slope, 16),
        'intercept': round(calibrator.intercept, 16),
        'r_value': round(calibrator.r_value, 16),
        'p_value': round(calibrator.p_value, 16),
        'std_err': round(calibrator.std_err, 16)
    }

    click.echo('Writing complete results to {}'.format(csv_file_name))
    write_csv(data, csv_file_name, header)

    click.echo('Calibrating density file')
    density = calibrator.slope * sitk.Cast(ct, sitk.sitkFloat32) + \
        calibrator.intercept

    click.echo('Writing density file to {}'.format(density_file_name))
    sitk.ReadImage(density, density_file_name)