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2,100 | SoftwareDefinedBuildings/XBOS | apps/Data_quality_analysis/Wrapper.py | Wrapper.search | def search(self, file_name, imported_data=None):
""" Run models on different data configurations.
Note
----
The input json file should include ALL parameters.
Parameters
----------
file_name : str
Optional json file to read parameters.
... | python | def search(self, file_name, imported_data=None):
""" Run models on different data configurations.
Note
----
The input json file should include ALL parameters.
Parameters
----------
file_name : str
Optional json file to read parameters.
... | [
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Note
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Optional json file to read parameters.
imported_data : pd.DataFrame()
Pandas Dataframe... | [
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2,101 | SoftwareDefinedBuildings/XBOS | apps/Data_quality_analysis/Wrapper.py | Wrapper.clean_data | def clean_data(self, data, rename_col=None, drop_col=None,
resample=True, freq='h', resampler='mean',
interpolate=True, limit=1, method='linear',
remove_na=True, remove_na_how='any',
remove_outliers=True, sd_val=3,
remov... | python | def clean_data(self, data, rename_col=None, drop_col=None,
resample=True, freq='h', resampler='mean',
interpolate=True, limit=1, method='linear',
remove_na=True, remove_na_how='any',
remove_outliers=True, sd_val=3,
remov... | [
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data : pd.DataFrame()
Dataframe to be cleaned.
rename_col : list(str)
List of new column names.
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2,102 | SoftwareDefinedBuildings/XBOS | dashboards/sitedash/app.py | prevmonday | def prevmonday(num):
"""
Return unix SECOND timestamp of "num" mondays ago
"""
today = get_today()
lastmonday = today - timedelta(days=today.weekday(), weeks=num)
return lastmonday | python | def prevmonday(num):
"""
Return unix SECOND timestamp of "num" mondays ago
"""
today = get_today()
lastmonday = today - timedelta(days=today.weekday(), weeks=num)
return lastmonday | [
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2,103 | SoftwareDefinedBuildings/XBOS | apps/consumption/iec.py | med_filt | def med_filt(x, k=201):
"""Apply a length-k median filter to a 1D array x.
Boundaries are extended by repeating endpoints.
"""
if x.ndim > 1:
x = np.squeeze(x)
med = np.median(x)
assert k % 2 == 1, "Median filter length must be odd."
assert x.ndim == 1, "Input must be one-dimensional... | python | def med_filt(x, k=201):
"""Apply a length-k median filter to a 1D array x.
Boundaries are extended by repeating endpoints.
"""
if x.ndim > 1:
x = np.squeeze(x)
med = np.median(x)
assert k % 2 == 1, "Median filter length must be odd."
assert x.ndim == 1, "Input must be one-dimensional... | [
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2,104 | SoftwareDefinedBuildings/XBOS | apps/data_analysis/XBOS_data_analytics/Wrapper.py | Wrapper.preprocess_data | def preprocess_data(self, data,
hdh_cpoint=65, cdh_cpoint=65, col_hdh_cdh=None,
col_degree=None, degree=None,
standardize=False, normalize=False,
year=False, month=False, week=False, tod=False, dow=False,
... | python | def preprocess_data(self, data,
hdh_cpoint=65, cdh_cpoint=65, col_hdh_cdh=None,
col_degree=None, degree=None,
standardize=False, normalize=False,
year=False, month=False, week=False, tod=False, dow=False,
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Parameters
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data : pd.DataFrame()
Dataframe to be preprocessed.
hdh_cpoint : int
Heating degree hours. Defaults to 65.
cdh_cpoin... | [
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2,105 | SoftwareDefinedBuildings/XBOS | apps/data_analysis/XBOS_data_analytics/Wrapper.py | Wrapper.model | def model(self, data,
ind_col=None, dep_col=None,
project_ind_col=None,
baseline_period=[None, None], projection_period=None, exclude_time_period=None,
alphas=np.logspace(-4,1,30),
cv=3, plot=True, figsize=None,
custom_model_func=None):
"""... | python | def model(self, data,
ind_col=None, dep_col=None,
project_ind_col=None,
baseline_period=[None, None], projection_period=None, exclude_time_period=None,
alphas=np.logspace(-4,1,30),
cv=3, plot=True, figsize=None,
custom_model_func=None):
"""... | [
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Dataframe to model.
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2,106 | SoftwareDefinedBuildings/XBOS | python/xbos/services/pundat.py | make_dataframe | def make_dataframe(result):
"""
Turns the results of one of the data API calls into a pandas dataframe
"""
import pandas as pd
ret = {}
if isinstance(result,dict):
if 'timeseries' in result:
result = result['timeseries']
for uuid, data in result.items():
df = pd.D... | python | def make_dataframe(result):
"""
Turns the results of one of the data API calls into a pandas dataframe
"""
import pandas as pd
ret = {}
if isinstance(result,dict):
if 'timeseries' in result:
result = result['timeseries']
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2,107 | SoftwareDefinedBuildings/XBOS | python/xbos/services/pundat.py | DataClient.query | def query(self, query, archiver="", timeout=DEFAULT_TIMEOUT):
"""
Runs the given pundat query and returns the results as a Python object.
Arguments:
[query]: the query string
[archiver]: if specified, this is the archiver to use. Else, it will run on the first archiver passed
... | python | def query(self, query, archiver="", timeout=DEFAULT_TIMEOUT):
"""
Runs the given pundat query and returns the results as a Python object.
Arguments:
[query]: the query string
[archiver]: if specified, this is the archiver to use. Else, it will run on the first archiver passed
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2,108 | SoftwareDefinedBuildings/XBOS | python/xbos/services/pundat.py | DataClient.uuids | def uuids(self, where, archiver="", timeout=DEFAULT_TIMEOUT):
"""
Using the given where-clause, finds all UUIDs that match
Arguments:
[where]: the where clause (e.g. 'path like "keti"', 'SourceName = "TED Main"')
[archiver]: if specified, this is the archiver to use. Else, it wi... | python | def uuids(self, where, archiver="", timeout=DEFAULT_TIMEOUT):
"""
Using the given where-clause, finds all UUIDs that match
Arguments:
[where]: the where clause (e.g. 'path like "keti"', 'SourceName = "TED Main"')
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2,109 | SoftwareDefinedBuildings/XBOS | python/xbos/services/pundat.py | DataClient.tags | def tags(self, where, archiver="", timeout=DEFAULT_TIMEOUT):
"""
Retrieves tags for all streams matching the given WHERE clause
Arguments:
[where]: the where clause (e.g. 'path like "keti"', 'SourceName = "TED Main"')
[archiver]: if specified, this is the archiver to use. Else, ... | python | def tags(self, where, archiver="", timeout=DEFAULT_TIMEOUT):
"""
Retrieves tags for all streams matching the given WHERE clause
Arguments:
[where]: the where clause (e.g. 'path like "keti"', 'SourceName = "TED Main"')
[archiver]: if specified, this is the archiver to use. Else, ... | [
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2,110 | SoftwareDefinedBuildings/XBOS | python/xbos/services/pundat.py | DataClient.tags_uuids | def tags_uuids(self, uuids, archiver="", timeout=DEFAULT_TIMEOUT):
"""
Retrieves tags for all streams with the provided UUIDs
Arguments:
[uuids]: list of UUIDs
[archiver]: if specified, this is the archiver to use. Else, it will run on the first archiver passed
... | python | def tags_uuids(self, uuids, archiver="", timeout=DEFAULT_TIMEOUT):
"""
Retrieves tags for all streams with the provided UUIDs
Arguments:
[uuids]: list of UUIDs
[archiver]: if specified, this is the archiver to use. Else, it will run on the first archiver passed
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2,111 | SoftwareDefinedBuildings/XBOS | python/xbos/services/pundat.py | DataClient.data | def data(self, where, start, end, archiver="", timeout=DEFAULT_TIMEOUT):
"""
With the given WHERE clause, retrieves all RAW data between the 2 given timestamps
Arguments:
[where]: the where clause (e.g. 'path like "keti"', 'SourceName = "TED Main"')
[start, end]: time references... | python | def data(self, where, start, end, archiver="", timeout=DEFAULT_TIMEOUT):
"""
With the given WHERE clause, retrieves all RAW data between the 2 given timestamps
Arguments:
[where]: the where clause (e.g. 'path like "keti"', 'SourceName = "TED Main"')
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2,112 | SoftwareDefinedBuildings/XBOS | python/xbos/services/pundat.py | DataClient.data_uuids | def data_uuids(self, uuids, start, end, archiver="", timeout=DEFAULT_TIMEOUT):
"""
With the given list of UUIDs, retrieves all RAW data between the 2 given timestamps
Arguments:
[uuids]: list of UUIDs
[start, end]: time references:
[archiver]: if specified, this is the a... | python | def data_uuids(self, uuids, start, end, archiver="", timeout=DEFAULT_TIMEOUT):
"""
With the given list of UUIDs, retrieves all RAW data between the 2 given timestamps
Arguments:
[uuids]: list of UUIDs
[start, end]: time references:
[archiver]: if specified, this is the a... | [
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2,113 | SoftwareDefinedBuildings/XBOS | python/xbos/services/pundat.py | DataClient.stats | def stats(self, where, start, end, pw, archiver="", timeout=DEFAULT_TIMEOUT):
"""
With the given WHERE clause, retrieves all statistical data between the 2 given timestamps, using the given pointwidth
Arguments:
[where]: the where clause (e.g. 'path like "keti"', 'SourceName = "TED Main... | python | def stats(self, where, start, end, pw, archiver="", timeout=DEFAULT_TIMEOUT):
"""
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2,115 | Danielhiversen/flux_led | flux_led/__main__.py | WifiLedBulb.brightness | def brightness(self):
"""Return current brightness 0-255.
For warm white return current led level. For RGB
calculate the HSV and return the 'value'.
"""
if self.mode == "ww":
return int(self.raw_state[9])
else:
_, _, v = colorsys.rgb_to_hsv(*self.... | python | def brightness(self):
"""Return current brightness 0-255.
For warm white return current led level. For RGB
calculate the HSV and return the 'value'.
"""
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2,117 | esheldon/fitsio | fitsio/util.py | cfitsio_version | def cfitsio_version(asfloat=False):
"""
Return the cfitsio version as a string.
"""
# use string version to avoid roundoffs
ver = '%0.3f' % _fitsio_wrap.cfitsio_version()
if asfloat:
return float(ver)
else:
return ver | python | def cfitsio_version(asfloat=False):
"""
Return the cfitsio version as a string.
"""
# use string version to avoid roundoffs
ver = '%0.3f' % _fitsio_wrap.cfitsio_version()
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Parameters
----------
array: numpy array
A numerical python array.
Returns
-------
Truth value:
True for little-endian
Notes
-----
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"""
Return True if array is little endian, False otherwise.
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array: numpy array
A numerical python array.
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2,119 | esheldon/fitsio | fitsio/util.py | array_to_native | def array_to_native(array, inplace=False):
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Convert an array to the native byte order.
NOTE: the inplace keyword argument is not currently used.
"""
if numpy.little_endian:
machine_little = True
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machine_little = False
data_little = False
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"""
Convert an array to the native byte order.
NOTE: the inplace keyword argument is not currently used.
"""
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2,120 | esheldon/fitsio | fitsio/util.py | mks | def mks(val):
"""
make sure the value is a string, paying mind to python3 vs 2
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sval = str(val)
return sval | python | def mks(val):
"""
make sure the value is a string, paying mind to python3 vs 2
"""
if sys.version_info > (3, 0, 0):
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2,121 | esheldon/fitsio | fitsio/hdu/table.py | _get_col_dimstr | def _get_col_dimstr(tdim, is_string=False):
"""
not for variable length
"""
dimstr = ''
if tdim is None:
dimstr = 'array[bad TDIM]'
else:
if is_string:
if len(tdim) > 1:
dimstr = [str(d) for d in tdim[1:]]
else:
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"""
not for variable length
"""
dimstr = ''
if tdim is None:
dimstr = 'array[bad TDIM]'
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2,122 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU.get_colname | def get_colname(self, colnum):
"""
Get the name associated with the given column number
parameters
----------
colnum: integer
The number for the column, zero offset
"""
if colnum < 0 or colnum > (len(self._colnames)-1):
raise ValueError(
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"""
Get the name associated with the given column number
parameters
----------
colnum: integer
The number for the column, zero offset
"""
if colnum < 0 or colnum > (len(self._colnames)-1):
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2,123 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU.write_column | def write_column(self, column, data, **keys):
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This HDU must be a table HDU.
parameters
----------
column: scalar string/integer
The column in which to write. Can be the name or number (0 offset)
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"""
Write data to a column in this HDU
This HDU must be a table HDU.
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----------
column: scalar string/integer
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2,124 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._verify_column_data | def _verify_column_data(self, colnum, data):
"""
verify the input data is of the correct type and shape
"""
this_dt = data.dtype.descr[0]
if len(data.shape) > 2:
this_shape = data.shape[1:]
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this_sha... | python | def _verify_column_data(self, colnum, data):
"""
verify the input data is of the correct type and shape
"""
this_dt = data.dtype.descr[0]
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2,125 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU.write_var_column | def write_var_column(self, column, data, firstrow=0, **keys):
"""
Write data to a variable-length column in this HDU
This HDU must be a table HDU.
parameters
----------
column: scalar string/integer
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"""
Write data to a variable-length column in this HDU
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column: scalar string/integer
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Insert a new column.
parameters
----------
name: string
The column name
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colnum: int, optional
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"""
Insert a new column.
parameters
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name: string
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2,127 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU.append | def append(self, data, **keys):
"""
Append new rows to a table HDU
parameters
----------
data: ndarray or list of arrays
A numerical python array with fields (recarray) or a list of
arrays. Should have the same fields as the existing table. If only
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"""
Append new rows to a table HDU
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data: ndarray or list of arrays
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2,128 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU.delete_rows | def delete_rows(self, rows):
"""
Delete rows from the table
parameters
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rows: sequence or slice
The exact rows to delete as a sequence, or a slice.
examples
--------
# delete a range of rows
with fitsio.FITS(fname,'r... | python | def delete_rows(self, rows):
"""
Delete rows from the table
parameters
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rows: sequence or slice
The exact rows to delete as a sequence, or a slice.
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Resize the table to the given size, removing or adding rows as
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Resize the table to the given size, removing or adding rows as
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2,130 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU.read | def read(self, **keys):
"""
read data from this HDU
By default, all data are read.
send columns= and rows= to select subsets of the data.
Table data are read into a recarray; use read_column() to get a single
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"""
read data from this HDU
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2,131 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._read_all | def _read_all(self, **keys):
"""
Read all data in the HDU.
parameters
----------
vstorage: string, optional
Over-ride the default method to store variable length columns. Can
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"""
Read all data in the HDU.
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vstorage: string, optional
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"""
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fits[ext][colname][rows]... | python | def read_column(self, col, **keys):
"""
Read the specified column
Alternatively, you can use slice notation
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Read the specified rows.
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A list or array of row indices.
vstorage: string, optional
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"""
Read the specified rows.
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2,134 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU.read_columns | def read_columns(self, columns, **keys):
"""
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read a subset of columns from this binary table HDU
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2,135 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU.read_slice | def read_slice(self, firstrow, lastrow, step=1, **keys):
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Read all rows between firstrow and lastrow (non-inclusive, as per
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para... | python | def read_slice(self, firstrow, lastrow, step=1, **keys):
"""
Read the specified row slice from a table.
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2,136 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU.get_rec_dtype | def get_rec_dtype(self, **keys):
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Get the dtype for the specified columns
parameters
----------
colnums: integer array
The column numbers, 0 offset
vstorage: string, optional
See docs in read_columns
"""
colnums = keys.get('coln... | python | def get_rec_dtype(self, **keys):
"""
Get the dtype for the specified columns
parameters
----------
colnums: integer array
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vstorage: string, optional
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2,137 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._check_tbit | def _check_tbit(self, **keys):
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parameters
----------
colnums: integer array, optional
"""
colnums = keys.get('colnums', None)
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colnums = self._extract_colnums()
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"""
Check if one of the columns is a TBIT column
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----------
colnums: integer array, optional
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2,138 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._fix_tbit_dtype | def _fix_tbit_dtype(self, array, colnums):
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parameters
----------
array: record array
colnums: column numbers for lookup
"""
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array: record array
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2,140 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU.get_rec_column_descr | def get_rec_column_descr(self, colnum, vstorage):
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colnum: integer
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vstorage: string
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2,141 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._read_rec_with_var | def _read_rec_with_var(
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2,142 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._extract_rows | def _extract_rows(self, rows):
"""
Extract an array of rows from an input scalar or sequence
"""
if rows is not None:
rows = numpy.array(rows, ndmin=1, copy=False, dtype='i8')
# returns unique, sorted
rows = numpy.unique(rows)
maxrow = sel... | python | def _extract_rows(self, rows):
"""
Extract an array of rows from an input scalar or sequence
"""
if rows is not None:
rows = numpy.array(rows, ndmin=1, copy=False, dtype='i8')
# returns unique, sorted
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2,143 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._process_slice | def _process_slice(self, arg):
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"""
process the input slice for use calling the C code
"""
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nrows = self._info['nrows']
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2,144 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._slice2rows | def _slice2rows(self, start, stop, step=None):
"""
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"""
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if start is None:
start = 0
if stop is None:
stop = nrows
if step is None:
step = 1
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"""
Convert a slice to an explicit array of rows
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start = 0
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2,145 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._fix_range | def _fix_range(self, num, isslice=True):
"""
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"""
nrows = self._info['nrows']
if isslice:
# include the end
if num < 0:
num = nrows + (1+num)
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"""
Ensure the input is within range.
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"""
nrows = self._info['nrows']
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2,146 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._rescale_and_convert_field_inplace | def _rescale_and_convert_field_inplace(self, array, name, scale, zero):
"""
Apply fits scalings. Also, convert bool to proper
numpy boolean values
"""
self._rescale_array(array[name], scale, zero)
if array[name].dtype == numpy.bool:
array[name] = self._conver... | python | def _rescale_and_convert_field_inplace(self, array, name, scale, zero):
"""
Apply fits scalings. Also, convert bool to proper
numpy boolean values
"""
self._rescale_array(array[name], scale, zero)
if array[name].dtype == numpy.bool:
array[name] = self._conver... | [
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2,147 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._rescale_array | def _rescale_array(self, array, scale, zero):
"""
Scale the input array
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sval = numpy.array(scale, dtype=array.dtype)
array *= sval
if zero != 0.0:
zval = numpy.array(zero, dtype=array.dtype)
array += zval | python | def _rescale_array(self, array, scale, zero):
"""
Scale the input array
"""
if scale != 1.0:
sval = numpy.array(scale, dtype=array.dtype)
array *= sval
if zero != 0.0:
zval = numpy.array(zero, dtype=array.dtype)
array += zval | [
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2,148 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._maybe_trim_strings | def _maybe_trim_strings(self, array, **keys):
"""
if requested, trim trailing white space from
all string fields in the input array
"""
trim_strings = keys.get('trim_strings', False)
if self.trim_strings or trim_strings:
_trim_strings(array) | python | def _maybe_trim_strings(self, array, **keys):
"""
if requested, trim trailing white space from
all string fields in the input array
"""
trim_strings = keys.get('trim_strings', False)
if self.trim_strings or trim_strings:
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2,149 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._get_tbl_numpy_dtype | def _get_tbl_numpy_dtype(self, colnum, include_endianness=True):
"""
Get numpy type for the input column
"""
table_type = self._info['hdutype']
table_type_string = _hdu_type_map[table_type]
try:
ftype = self._info['colinfo'][colnum]['eqtype']
if ta... | python | def _get_tbl_numpy_dtype(self, colnum, include_endianness=True):
"""
Get numpy type for the input column
"""
table_type = self._info['hdutype']
table_type_string = _hdu_type_map[table_type]
try:
ftype = self._info['colinfo'][colnum]['eqtype']
if ta... | [
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2,150 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._process_args_as_rows_or_columns | def _process_args_as_rows_or_columns(self, arg, unpack=False):
"""
We must be able to interpret the args as as either a column name or
row number, or sequences thereof. Numpy arrays and slices are also
fine.
Examples:
'field'
35
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... | python | def _process_args_as_rows_or_columns(self, arg, unpack=False):
"""
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Examples:
'field'
35
[35,55,86]
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2,151 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._extract_colnums | def _extract_colnums(self, columns=None):
"""
Extract an array of columns from the input
"""
if columns is None:
return numpy.arange(self._ncol, dtype='i8')
if not isinstance(columns, (tuple, list, numpy.ndarray)):
# is a scalar
return self._e... | python | def _extract_colnums(self, columns=None):
"""
Extract an array of columns from the input
"""
if columns is None:
return numpy.arange(self._ncol, dtype='i8')
if not isinstance(columns, (tuple, list, numpy.ndarray)):
# is a scalar
return self._e... | [
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2,152 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._extract_colnum | def _extract_colnum(self, col):
"""
Get the column number for the input column
"""
if isinteger(col):
colnum = col
if (colnum < 0) or (colnum > (self._ncol-1)):
raise ValueError(
"column number should be in [0,%d]" % (0, self._... | python | def _extract_colnum(self, col):
"""
Get the column number for the input column
"""
if isinteger(col):
colnum = col
if (colnum < 0) or (colnum > (self._ncol-1)):
raise ValueError(
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2,153 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._update_info | def _update_info(self):
"""
Call parent method and make sure this is in fact a
table HDU. Set some convenience data.
"""
super(TableHDU, self)._update_info()
if self._info['hdutype'] == IMAGE_HDU:
mess = "Extension %s is not a Table HDU" % self.ext
... | python | def _update_info(self):
"""
Call parent method and make sure this is in fact a
table HDU. Set some convenience data.
"""
super(TableHDU, self)._update_info()
if self._info['hdutype'] == IMAGE_HDU:
mess = "Extension %s is not a Table HDU" % self.ext
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2,154 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._get_next_buffered_row | def _get_next_buffered_row(self):
"""
Get the next row for iteration.
"""
if self._iter_row == self._iter_nrows:
raise StopIteration
if self._row_buffer_index >= self._iter_row_buffer:
self._buffer_iter_rows(self._iter_row)
data = self._row_buffe... | python | def _get_next_buffered_row(self):
"""
Get the next row for iteration.
"""
if self._iter_row == self._iter_nrows:
raise StopIteration
if self._row_buffer_index >= self._iter_row_buffer:
self._buffer_iter_rows(self._iter_row)
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2,155 | esheldon/fitsio | fitsio/hdu/table.py | TableHDU._buffer_iter_rows | def _buffer_iter_rows(self, start):
"""
Read in the buffer for iteration
"""
self._row_buffer = self[start:start+self._iter_row_buffer]
# start back at the front of the buffer
self._row_buffer_index = 0 | python | def _buffer_iter_rows(self, start):
"""
Read in the buffer for iteration
"""
self._row_buffer = self[start:start+self._iter_row_buffer]
# start back at the front of the buffer
self._row_buffer_index = 0 | [
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2,156 | esheldon/fitsio | fitsio/hdu/table.py | AsciiTableHDU.read | def read(self, **keys):
"""
read a data from an ascii table HDU
By default, all rows are read. Send rows= to select subsets of the
data. Table data are read into a recarray for multiple columns,
plain array for a single column.
parameters
----------
co... | python | def read(self, **keys):
"""
read a data from an ascii table HDU
By default, all rows are read. Send rows= to select subsets of the
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2,157 | esheldon/fitsio | fitsio/hdu/table.py | TableColumnSubset.read | def read(self, **keys):
"""
Read the data from disk and return as a numpy array
"""
if self.is_scalar:
data = self.fitshdu.read_column(self.columns, **keys)
else:
c = keys.get('columns', None)
if c is None:
keys['columns'] = se... | python | def read(self, **keys):
"""
Read the data from disk and return as a numpy array
"""
if self.is_scalar:
data = self.fitshdu.read_column(self.columns, **keys)
else:
c = keys.get('columns', None)
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2,158 | esheldon/fitsio | fitsio/fitslib.py | read | def read(filename, ext=None, extver=None, **keys):
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"""
Convenience function to read data from the specified FITS HDU
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2,159 | esheldon/fitsio | fitsio/fitslib.py | read_header | def read_header(filename, ext=0, extver=None, case_sensitive=False, **keys):
"""
Convenience function to read the header from the specified FITS HDU
The FITSHDR allows access to the values and comments by name and
number.
parameters
----------
filename: string
A filename.
ext: ... | python | def read_header(filename, ext=0, extver=None, case_sensitive=False, **keys):
"""
Convenience function to read the header from the specified FITS HDU
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filename: string
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2,160 | esheldon/fitsio | fitsio/fitslib.py | read_scamp_head | def read_scamp_head(fname, header=None):
"""
read a SCAMP .head file as a fits header FITSHDR object
parameters
----------
fname: string
The path to the SCAMP .head file
header: FITSHDR, optional
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be any obj... | python | def read_scamp_head(fname, header=None):
"""
read a SCAMP .head file as a fits header FITSHDR object
parameters
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fname: string
The path to the SCAMP .head file
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2,161 | esheldon/fitsio | fitsio/fitslib.py | write | def write(filename, data, extname=None, extver=None, units=None,
compress=None, table_type='binary', header=None,
clobber=False, **keys):
"""
Convenience function to create a new HDU and write the data.
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compress=None, table_type='binary', header=None,
clobber=False, **keys):
"""
Convenience function to create a new HDU and write the data.
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2,162 | esheldon/fitsio | fitsio/fitslib.py | array2tabledef | def array2tabledef(data, table_type='binary', write_bitcols=False):
"""
Similar to descr2tabledef but if there are object columns a type
and max length will be extracted and used for the tabledef
"""
is_ascii = (table_type == 'ascii')
if data.dtype.fields is None:
raise ValueError("data... | python | def array2tabledef(data, table_type='binary', write_bitcols=False):
"""
Similar to descr2tabledef but if there are object columns a type
and max length will be extracted and used for the tabledef
"""
is_ascii = (table_type == 'ascii')
if data.dtype.fields is None:
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2,163 | esheldon/fitsio | fitsio/fitslib.py | descr2tabledef | def descr2tabledef(descr, table_type='binary', write_bitcols=False):
"""
Create a FITS table def from the input numpy descriptor.
parameters
----------
descr: list
A numpy recarray type descriptor array.dtype.descr
returns
-------
names, formats, dims: tuple of lists
T... | python | def descr2tabledef(descr, table_type='binary', write_bitcols=False):
"""
Create a FITS table def from the input numpy descriptor.
parameters
----------
descr: list
A numpy recarray type descriptor array.dtype.descr
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names, formats, dims: tuple of lists
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2,164 | esheldon/fitsio | fitsio/fitslib.py | get_tile_dims | def get_tile_dims(tile_dims, imshape):
"""
Just make sure the tile dims has the appropriate number of dimensions
"""
if tile_dims is None:
td = None
else:
td = numpy.array(tile_dims, dtype='i8')
nd = len(imshape)
if td.size != nd:
msg = "expected tile_dim... | python | def get_tile_dims(tile_dims, imshape):
"""
Just make sure the tile dims has the appropriate number of dimensions
"""
if tile_dims is None:
td = None
else:
td = numpy.array(tile_dims, dtype='i8')
nd = len(imshape)
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2,165 | esheldon/fitsio | fitsio/fitslib.py | _extract_table_type | def _extract_table_type(type):
"""
Get the numerical table type
"""
if isinstance(type, str):
type = type.lower()
if type[0:7] == 'binary':
table_type = BINARY_TBL
elif type[0:6] == 'ascii':
table_type = ASCII_TBL
else:
raise ValueError... | python | def _extract_table_type(type):
"""
Get the numerical table type
"""
if isinstance(type, str):
type = type.lower()
if type[0:7] == 'binary':
table_type = BINARY_TBL
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table_type = ASCII_TBL
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2,166 | esheldon/fitsio | fitsio/fitslib.py | FITS.close | def close(self):
"""
Close the fits file and set relevant metadata to None
"""
if hasattr(self, '_FITS'):
if self._FITS is not None:
self._FITS.close()
self._FITS = None
self._filename = None
self.mode = None
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"""
Close the fits file and set relevant metadata to None
"""
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2,167 | esheldon/fitsio | fitsio/fitslib.py | FITS.movnam_hdu | def movnam_hdu(self, extname, hdutype=ANY_HDU, extver=0):
"""
Move to the indicated HDU by name
In general, it is not necessary to use this method explicitly.
returns the one-offset extension number
"""
extname = mks(extname)
hdu = self._FITS.movnam_hdu(hdutype,... | python | def movnam_hdu(self, extname, hdutype=ANY_HDU, extver=0):
"""
Move to the indicated HDU by name
In general, it is not necessary to use this method explicitly.
returns the one-offset extension number
"""
extname = mks(extname)
hdu = self._FITS.movnam_hdu(hdutype,... | [
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2,168 | esheldon/fitsio | fitsio/fitslib.py | FITS.reopen | def reopen(self):
"""
close and reopen the fits file with the same mode
"""
self._FITS.close()
del self._FITS
self._FITS = _fitsio_wrap.FITS(self._filename, self.intmode, 0)
self.update_hdu_list() | python | def reopen(self):
"""
close and reopen the fits file with the same mode
"""
self._FITS.close()
del self._FITS
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2,169 | esheldon/fitsio | fitsio/fitslib.py | FITS.write | def write(self, data, units=None, extname=None, extver=None,
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"""
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2,170 | esheldon/fitsio | fitsio/fitslib.py | FITS.write_image | def write_image(self, img, extname=None, extver=None,
compress=None, tile_dims=None, header=None):
"""
Create a new image extension and write the data.
parameters
----------
img: ndarray
An n-dimensional image.
extname: string, optional
... | python | def write_image(self, img, extname=None, extver=None,
compress=None, tile_dims=None, header=None):
"""
Create a new image extension and write the data.
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img: ndarray
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2,171 | esheldon/fitsio | fitsio/fitslib.py | FITS.create_image_hdu | def create_image_hdu(self,
img=None,
dims=None,
dtype=None,
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tile_dims=None,
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2,172 | esheldon/fitsio | fitsio/fitslib.py | FITS._ensure_empty_image_ok | def _ensure_empty_image_ok(self):
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HDU and if there is no data there already
"""
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"""
If ignore_empty was not set to True, we only allow empty HDU for first
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2,173 | esheldon/fitsio | fitsio/fitslib.py | FITS.write_table | def write_table(self, data, table_type='binary',
names=None, formats=None, units=None,
extname=None, extver=None, header=None,
write_bitcols=False):
"""
Create a new table extension and write the data.
The table definition is taken fro... | python | def write_table(self, data, table_type='binary',
names=None, formats=None, units=None,
extname=None, extver=None, header=None,
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2,174 | esheldon/fitsio | fitsio/fitslib.py | FITS.create_table_hdu | def create_table_hdu(self, data=None, dtype=None,
header=None,
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header=None,
names=None, formats=None,
units=None, dims=None, extname=None, extver=None,
table_type='binary', write_bitcols=False):
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2,175 | esheldon/fitsio | fitsio/fitslib.py | FITS.update_hdu_list | def update_hdu_list(self, rebuild=True):
"""
Force an update of the entire HDU list
Normally you don't need to call this method directly
if rebuild is false or the hdu_list is not yet set, the list is
rebuilt from scratch
"""
if not hasattr(self, 'hdu_list'):
... | python | def update_hdu_list(self, rebuild=True):
"""
Force an update of the entire HDU list
Normally you don't need to call this method directly
if rebuild is false or the hdu_list is not yet set, the list is
rebuilt from scratch
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2,176 | esheldon/fitsio | fitsio/fitslib.py | FITS.next | def next(self):
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"""
if self._iter_index == len(self.hdu_list):
raise StopIteration
hdu = self.hdu_list[self._iter_index]
self._iter_index += 1
return hdu | python | def next(self):
"""
Move to the next iteration
"""
if self._iter_index == len(self.hdu_list):
raise StopIteration
hdu = self.hdu_list[self._iter_index]
self._iter_index += 1
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2,177 | esheldon/fitsio | fitsio/fitslib.py | FITS._extract_item | def _extract_item(self, item):
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2,178 | esheldon/fitsio | fitsio/hdu/image.py | ImageHDU._update_info | def _update_info(self):
"""
Call parent method and make sure this is in fact a
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"""
super(ImageHDU, self)._update_info()
if self._info['hdutype'] != IMAGE_HDU:
mess = "Extension %s is not a Image HDU" % self.ext
rais... | python | def _update_info(self):
"""
Call parent method and make sure this is in fact a
image HDU. Set dims in C order
"""
super(ImageHDU, self)._update_info()
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2,179 | esheldon/fitsio | fitsio/hdu/image.py | ImageHDU.reshape | def reshape(self, dims):
"""
reshape an existing image to the requested dimensions
parameters
----------
dims: sequence
Any sequence convertible to i8
"""
adims = numpy.array(dims, ndmin=1, dtype='i8')
self._FITS.reshape_image(self._ext+1, ad... | python | def reshape(self, dims):
"""
reshape an existing image to the requested dimensions
parameters
----------
dims: sequence
Any sequence convertible to i8
"""
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2,180 | esheldon/fitsio | fitsio/hdu/image.py | ImageHDU.write | def write(self, img, start=0, **keys):
"""
Write the image into this HDU
If data already exist in this HDU, they will be overwritten. If the
image to write is larger than the image on disk, or if the start
position is such that the write would extend beyond the existing
... | python | def write(self, img, start=0, **keys):
"""
Write the image into this HDU
If data already exist in this HDU, they will be overwritten. If the
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2,181 | esheldon/fitsio | fitsio/hdu/image.py | ImageHDU.read | def read(self, **keys):
"""
Read the image.
If the HDU is an IMAGE_HDU, read the corresponding image. Compression
and scaling are dealt with properly.
"""
if not self.has_data():
return None
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array =... | python | def read(self, **keys):
"""
Read the image.
If the HDU is an IMAGE_HDU, read the corresponding image. Compression
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"""
if not self.has_data():
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2,182 | esheldon/fitsio | fitsio/hdu/image.py | ImageHDU._get_dtype_and_shape | def _get_dtype_and_shape(self):
"""
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if self._info['ndims'] != 0:
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raise IOError("no image present in HDU")
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"""
Get the numpy dtype and shape for image
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2,183 | esheldon/fitsio | fitsio/hdu/image.py | ImageHDU._get_image_numpy_dtype | def _get_image_numpy_dtype(self):
"""
Get the numpy dtype for the image
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ftype = self._info['img_equiv_type']
npy_type = _image_bitpix2npy[ftype]
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Get the numpy dtype for the image
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2,184 | esheldon/fitsio | fitsio/hdu/image.py | ImageHDU._read_image_slice | def _read_image_slice(self, arg):
"""
workhorse to read a slice
"""
if 'ndims' not in self._info:
raise ValueError("Attempt to slice empty extension")
if isinstance(arg, slice):
# one-dimensional, e.g. 2:20
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2,185 | esheldon/fitsio | fitsio/hdu/image.py | ImageHDU._expand_if_needed | def _expand_if_needed(self, dims, write_dims, start, offset):
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expand the on-disk image if the indended write will extend
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"""
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expand the on-disk image if the indended write will extend
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2,186 | esheldon/fitsio | fitsio/hdu/base.py | HDUBase.get_extname | def get_extname(self):
"""
Get the name for this extension, can be an empty string
"""
name = self._info['extname']
if name.strip() == '':
name = self._info['hduname']
return name.strip() | python | def get_extname(self):
"""
Get the name for this extension, can be an empty string
"""
name = self._info['extname']
if name.strip() == '':
name = self._info['hduname']
return name.strip() | [
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2,187 | esheldon/fitsio | fitsio/hdu/base.py | HDUBase.get_extver | def get_extver(self):
"""
Get the version for this extension.
Used when a name is given to multiple extensions
"""
ver = self._info['extver']
if ver == 0:
ver = self._info['hduver']
return ver | python | def get_extver(self):
"""
Get the version for this extension.
Used when a name is given to multiple extensions
"""
ver = self._info['extver']
if ver == 0:
ver = self._info['hduver']
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2,188 | esheldon/fitsio | fitsio/hdu/base.py | HDUBase.get_exttype | def get_exttype(self, num=False):
"""
Get the extension type
By default the result is a string that mirrors
the enumerated type names in cfitsio
'IMAGE_HDU', 'ASCII_TBL', 'BINARY_TBL'
which have numeric values
0 1 2
send num=True to get the number... | python | def get_exttype(self, num=False):
"""
Get the extension type
By default the result is a string that mirrors
the enumerated type names in cfitsio
'IMAGE_HDU', 'ASCII_TBL', 'BINARY_TBL'
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2,189 | esheldon/fitsio | fitsio/hdu/base.py | HDUBase.verify_checksum | def verify_checksum(self):
"""
Verify the checksum in the header for this HDU.
"""
res = self._FITS.verify_checksum(self._ext+1)
if res['dataok'] != 1:
raise ValueError("data checksum failed")
if res['hduok'] != 1:
raise ValueError("hdu checksum fa... | python | def verify_checksum(self):
"""
Verify the checksum in the header for this HDU.
"""
res = self._FITS.verify_checksum(self._ext+1)
if res['dataok'] != 1:
raise ValueError("data checksum failed")
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2,190 | esheldon/fitsio | fitsio/hdu/base.py | HDUBase.write_comment | def write_comment(self, comment):
"""
Write a comment into the header
"""
self._FITS.write_comment(self._ext+1, str(comment)) | python | def write_comment(self, comment):
"""
Write a comment into the header
"""
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2,191 | esheldon/fitsio | fitsio/hdu/base.py | HDUBase.write_key | def write_key(self, name, value, comment=""):
"""
Write the input value to the header
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----------
name: string
Name of keyword to write/update
value: scalar
Value to write, can be string float or integer type,
including numpy... | python | def write_key(self, name, value, comment=""):
"""
Write the input value to the header
parameters
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name: string
Name of keyword to write/update
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Value to write, can be string float or integer type,
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2,192 | esheldon/fitsio | fitsio/hdu/base.py | HDUBase.write_keys | def write_keys(self, records_in, clean=True):
"""
Write the keywords to the header.
parameters
----------
records: FITSHDR or list or dict
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"""
Write the keywords to the header.
parameters
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records: FITSHDR or list or dict
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2,193 | esheldon/fitsio | fitsio/hdu/base.py | HDUBase._update_info | def _update_info(self):
"""
Update metadata for this HDU
"""
try:
self._FITS.movabs_hdu(self._ext+1)
except IOError:
raise RuntimeError("no such hdu")
self._info = self._FITS.get_hdu_info(self._ext+1) | python | def _update_info(self):
"""
Update metadata for this HDU
"""
try:
self._FITS.movabs_hdu(self._ext+1)
except IOError:
raise RuntimeError("no such hdu")
self._info = self._FITS.get_hdu_info(self._ext+1) | [
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2,194 | esheldon/fitsio | fitsio/hdu/base.py | HDUBase._get_repr_list | def _get_repr_list(self):
"""
Get some representation data common to all HDU types
"""
spacing = ' '*2
text = ['']
text.append("%sfile: %s" % (spacing, self._filename))
text.append("%sextension: %d" % (spacing, self._info['hdunum']-1))
text.append(
... | python | def _get_repr_list(self):
"""
Get some representation data common to all HDU types
"""
spacing = ' '*2
text = ['']
text.append("%sfile: %s" % (spacing, self._filename))
text.append("%sextension: %d" % (spacing, self._info['hdunum']-1))
text.append(
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2,195 | esheldon/fitsio | fitsio/header.py | FITSHDR.add_record | def add_record(self, record_in):
"""
Add a new record. Strip quotes from around strings.
This will over-write if the key already exists, except
for COMMENT and HISTORY fields
parameters
-----------
record:
The record, either a dict or a header card ... | python | def add_record(self, record_in):
"""
Add a new record. Strip quotes from around strings.
This will over-write if the key already exists, except
for COMMENT and HISTORY fields
parameters
-----------
record:
The record, either a dict or a header card ... | [
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2,196 | esheldon/fitsio | fitsio/header.py | FITSHDR.get_comment | def get_comment(self, item):
"""
Get the comment for the requested entry
"""
key = item.upper()
if key not in self._record_map:
raise KeyError("unknown record: %s" % key)
if 'comment' not in self._record_map[key]:
return None
else:
... | python | def get_comment(self, item):
"""
Get the comment for the requested entry
"""
key = item.upper()
if key not in self._record_map:
raise KeyError("unknown record: %s" % key)
if 'comment' not in self._record_map[key]:
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2,197 | esheldon/fitsio | fitsio/header.py | FITSHDR.delete | def delete(self, name):
"""
Delete the specified entry if it exists.
"""
if isinstance(name, (list, tuple)):
for xx in name:
self.delete(xx)
else:
if name in self._record_map:
del self._record_map[name]
self.... | python | def delete(self, name):
"""
Delete the specified entry if it exists.
"""
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2,198 | esheldon/fitsio | fitsio/header.py | FITSHDR.clean | def clean(self, is_table=False):
"""
Remove reserved keywords from the header.
These are keywords that the fits writer must write in order
to maintain consistency between header and data.
keywords
--------
is_table: bool, optional
Set True if this is... | python | def clean(self, is_table=False):
"""
Remove reserved keywords from the header.
These are keywords that the fits writer must write in order
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keywords
--------
is_table: bool, optional
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2,199 | esheldon/fitsio | fitsio/header.py | FITSHDR.get | def get(self, item, default_value=None):
"""
Get the requested header entry by keyword name
"""
found, name = self._contains_and_name(item)
if found:
return self._record_map[name]['value']
else:
return default_value | python | def get(self, item, default_value=None):
"""
Get the requested header entry by keyword name
"""
found, name = self._contains_and_name(item)
if found:
return self._record_map[name]['value']
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