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SF.net SVN: matplotlib: [5545] trunk/toolkits/basemap
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From: <js...@us...> - 2008-06-14 21:14:38
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Revision: 5545
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=5545&view=rev
Author: jswhit
Date: 2008-06-14 14:14:34 -0700 (Sat, 14 Jun 2008)
Log Message:
-----------
more docstring cleanups.
don't use PyNIO in NetCDFFile.
Modified Paths:
--------------
trunk/toolkits/basemap/Changelog
trunk/toolkits/basemap/lib/mpl_toolkits/basemap/__init__.py
trunk/toolkits/basemap/lib/mpl_toolkits/basemap/pupynere.py
Modified: trunk/toolkits/basemap/Changelog
===================================================================
--- trunk/toolkits/basemap/Changelog 2008-06-14 16:35:55 UTC (rev 5544)
+++ trunk/toolkits/basemap/Changelog 2008-06-14 21:14:34 UTC (rev 5545)
@@ -1,3 +1,5 @@
+ * don't try to use PyNIO in NetCDFFile (it was causing
+ too many suprises).
* improved documentation using Sphinx/docutils.
* change default behaviour of num2date and date2num to be
the same as matplotlib counterparts.
Modified: trunk/toolkits/basemap/lib/mpl_toolkits/basemap/__init__.py
===================================================================
--- trunk/toolkits/basemap/lib/mpl_toolkits/basemap/__init__.py 2008-06-14 16:35:55 UTC (rev 5544)
+++ trunk/toolkits/basemap/lib/mpl_toolkits/basemap/__init__.py 2008-06-14 21:14:34 UTC (rev 5545)
@@ -161,7 +161,8 @@
(because either they are computed internally, or entire globe is
always plotted).
- For the cylindrical projections(``cyl``, ``merc`` and ``mill``), the default is to use
+ For the cylindrical projections (``cyl``, ``merc`` and ``mill``),
+ the default is to use
llcrnrlon=-180,llcrnrlat=-90, urcrnrlon=180 and urcrnrlat=90). For all other
projections except ``ortho`` and ``geos``, either the lat/lon values of the
corners or width and height must be specified by the user.
@@ -3192,42 +3193,51 @@
def interp(datain,xin,yin,xout,yout,checkbounds=False,masked=False,order=1):
"""
- dataout = interp(datain,xin,yin,xout,yout,order=1)
+ Interpolate data (``datain``) on a rectilinear grid (with x = ``xin``
+ y = ``yin``) to a grid with x = ``xout``, y= ``yout``.
- interpolate data (datain) on a rectilinear grid (with x=xin
- y=yin) to a grid with x=xout, y=yout.
+ ============== ====================================================
+ Arguments Description
+ ============== ====================================================
+ datain a rank-2 array with 1st dimension corresponding to
+ y, 2nd dimension x.
+ xin, yin rank-1 arrays containing x and y of
+ datain grid in increasing order.
+ xout, yout rank-2 arrays containing x and y of desired output
+ grid.
+ ============== ====================================================
- datain is a rank-2 array with 1st dimension corresponding to y,
- 2nd dimension x.
+ ============== ====================================================
+ Keywords Description
+ ============== ====================================================
+ checkbounds If True, values of xout and yout are checked to see
+ that they lie within the range specified by xin
+ and xin.
+ If False, and xout,yout are outside xin,yin,
+ interpolated values will be clipped to values on
+ boundary of input grid (xin,yin)
+ Default is False.
+ masked If True, points outside the range of xin and yin
+ are masked (in a masked array).
+ If masked is set to a number, then
+ points outside the range of xin and yin will be
+ set to that number. Default False.
+ order 0 for nearest-neighbor interpolation, 1 for
+ bilinear interpolation (default 1).
+ ============== ====================================================
- xin, yin are rank-1 arrays containing x and y of
- datain grid in increasing order.
+ .. note::
+ If datain is a masked array and order=1 (bilinear interpolation) is
+ used, elements of dataout will be masked if any of the four surrounding
+ points in datain are masked. To avoid this, do the interpolation in two
+ passes, first with order=1 (producing dataout1), then with order=0
+ (producing dataout2). Then replace all the masked values in dataout1
+ with the corresponding elements in dataout2 (using numpy.where).
+ This effectively uses nearest neighbor interpolation if any of the
+ four surrounding points in datain are masked, and bilinear interpolation
+ otherwise.
- xout, yout are rank-2 arrays containing x and y of desired output grid.
-
- If checkbounds=True, values of xout and yout are checked to see that
- they lie within the range specified by xin and xin. Default is False.
-
- If checkbounds=False, and xout,yout are outside xin,yin, interpolated
- values will be clipped to values on boundary of input grid (xin,yin)
- if masked=False.
-
- If masked=True, the return value will be a masked
- array with those points masked. If masked is set to a number, then
- points outside the range of xin and yin will be set to that number.
-
- The order keyword can be 0 for nearest-neighbor interpolation,
- or 1 for bilinear interpolation (default 1).
-
- If datain is a masked array and order=1 (bilinear interpolation) is
- used, elements of dataout will be masked if any of the four surrounding
- points in datain are masked. To avoid this, do the interpolation in two
- passes, first with order=1 (producing dataout1), then with order=0
- (producing dataout2). Then replace all the masked values in dataout1
- with the corresponding elements in dataout2 (using numpy.where).
- This effectively uses nearest neighbor interpolation if any of the
- four surrounding points in datain are masked, and bilinear interpolation
- otherwise.
+ Returns ``dataout``, the interpolated data on the grid ``xout, yout``.
"""
# xin and yin must be monotonically increasing.
if xin[-1]-xin[0] < 0 or yin[-1]-yin[0] < 0:
@@ -3311,21 +3321,28 @@
def shiftgrid(lon0,datain,lonsin,start=True):
"""
- shift global lat/lon grid east or west.
+ Shift global lat/lon grid east or west.
assumes wraparound (or cyclic point) is included.
- lon0: starting longitude for shifted grid
- (ending longitude if start=False). lon0 must be on
- input grid (within the range of lonsin).
+ ============== ====================================================
+ Arguments Description
+ ============== ====================================================
+ lon0 starting longitude for shifted grid
+ (ending longitude if start=False). lon0 must be on
+ input grid (within the range of lonsin).
+ datain original data.
+ lonsin original longitudes.
+ ============== ====================================================
- datain: original data.
+ ============== ====================================================
+ Keywords Description
+ ============== ====================================================
+ start if True, lon0 represents the starting longitude
+ of the new grid. if False, lon0 is the ending
+ longitude. Default True.
+ ============== ====================================================
- lonsin: original longitudes.
-
- start[True]: if True, lon0 represents the starting longitude
- of the new grid. if False, lon0 is the ending longitude.
-
- returns dataout,lonsout (data and longitudes on shifted grid).
+ returns ``dataout,lonsout`` (data and longitudes on shifted grid).
"""
if np.fabs(lonsin[-1]-lonsin[0]-360.) > 1.e-4:
raise ValueError, 'cyclic point not included'
@@ -3348,9 +3365,8 @@
def addcyclic(arrin,lonsin):
"""
- arrout, lonsout = addcyclic(arrin, lonsin)
-
- Add cyclic (wraparound) point in longitude.
+ ``arrout, lonsout = addcyclic(arrin, lonsin)``
+ adds cyclic (wraparound) point in longitude to ``arrin`` and ``lonsin``.
"""
nlats = arrin.shape[0]
nlons = arrin.shape[1]
@@ -3383,85 +3399,71 @@
else:
return corners
-has_pynio = True
-try:
- from PyNGL import nio
-except ImportError:
- has_pynio = False
-
def NetCDFFile(file, maskandscale=True):
"""NetCDF File reader. API is the same as Scientific.IO.NetCDF.
- If 'file' is a URL that starts with 'http', it is assumed
+ If ``file`` is a URL that starts with `http`, it is assumed
to be a remote OPenDAP dataset, and the python dap client is used
to retrieve the data. Only the OPenDAP Array and Grid data
- types are recognized. If file does not start with 'http', it
- is assumed to be a local file. If possible, the file will be read
- with a pure python NetCDF reader, otherwise PyNIO
- (http://www.pyngl.ucar.edu/Nio.shtml) will be used (if it is installed).
- PyNIO supports NetCDF version 4, GRIB1, GRIB2, HDF4 and HDFEOS2 files.
- Data read from OPenDAP and NetCDF version 3 datasets will
+ types are recognized. If file does not start with `http`, it
+ is assumed to be a local netCDF file. Data will
automatically be converted to masked arrays if the variable has either
- a 'missing_value' or '_FillValue' attribute, and some data points
+ a ``missing_value`` or ``_FillValue`` attribute, and some data points
are equal to the value specified by that attribute. In addition,
- variables stored as integers that have the 'scale_factor' and
- 'add_offset' attribute will automatically be rescaled to floats when
- read. If PyNIO is used, neither of the automatic conversions will
- be performed. To suppress these automatic conversions, set the
- maskandscale keyword to False.
+ variables stored as integers that have the ``scale_factor`` and
+ ``add_offset`` attribute will automatically be rescaled to floats when
+ read. To suppress these automatic conversions, set the
+ ``maskandscale`` keyword to False.
"""
if file.startswith('http'):
return pupynere._RemoteFile(file,maskandscale)
else:
- # use pynio if it is installed and the file cannot
- # be read with the pure python netCDF reader. This allows
- # netCDF version 4, GRIB1, GRIB2, HDF4 and HDFEOS files
- # to be read.
- if has_pynio:
- try:
- f = pupynere._LocalFile(file,maskandscale)
- except:
- f = nio.open_file(file)
- # otherwise, use the pupynere netCDF 3 pure python reader.
- # (will fail if file is not a netCDF version 3 file).
- else:
- f = pupynere._LocalFile(file,maskandscale)
- return f
+ return pupynere._LocalFile(file,maskandscale)
def num2date(times,units='days since 0001-01-01 00:00:00',calendar='proleptic_gregorian'):
"""
Return datetime objects given numeric time values. The units
- of the numeric time values are described by the units argument
- and the calendar keyword. The returned datetime objects represent
+ of the numeric time values are described by the ``units`` argument
+ and the ``calendar`` keyword. The returned datetime objects represent
UTC with no time-zone offset, even if the specified
units contain a time-zone offset.
- Default behavior is the same as the matplotlib num2date function
+ Default behavior is the same as the matplotlib.dates.num2date function
but the reference time and calendar can be changed via the
- 'units' and 'calendar' keywords.
+ ``units`` and ``calendar`` keywords.
- Arguments:
+ ============== ====================================================
+ Arguments Description
+ ============== ====================================================
+ times numeric time values. Maximum resolution is 1 second.
+ ============== ====================================================
- times - numeric time values. Maximum resolution is 1 second.
+ ============== ====================================================
+ Keywords Description
+ ============== ====================================================
+ units a string of the form '<time units> since
+ <reference time>' describing the units and
+ origin of the time coordinate.
+ <time units> can be days, hours, minutes
+ or seconds. <reference time> is the time origin.
+ Default is 'days since 0001-01-01 00:00:00'.
+ calendar describes the calendar used in the time
+ calculations. All the values currently defined in
+ the CF metadata convention
+ (http://cf-pcmdi.llnl.gov/documents/cf-conventions/)
+ are supported.
+ Valid calendars ``standard``, ``gregorian``,
+ ``proleptic_gregorian``, ``noleap``, ``365_day``,
+ ``julian``, ``all_leap``, ``366_day``.
+ Default is ``proleptic_gregorian``.
+ ============== ====================================================
- units - a string of the form '<time units> since <reference time>'
- describing the time units. <time units> can be days, hours, minutes
- or seconds. <reference time> is the time origin.
- Default is 'days since 0001-01-01 00:00:00'.
-
- calendar - describes the calendar used in the time calculations.
- All the values currently defined in the CF metadata convention
- (http://cf-pcmdi.llnl.gov/documents/cf-conventions/) are supported.
- Valid calendars 'standard', 'gregorian', 'proleptic_gregorian'
- 'noleap', '365_day', '360_day', 'julian', 'all_leap', '366_day'.
- Default is 'standard'/'gregorian', which is a mixed
- Julian/Gregorian calendar. Defalut 'proleptic_gregorian'.
-
Returns a datetime instance, or an array of datetime instances.
The datetime instances returned are 'real' python datetime
objects if the date falls in the Gregorian calendar (i.e.
- calendar='proleptic_gregorian', or calendar = 'standard' or 'gregorian'
- and the date is after 1582-10-15). Otherwise, they are 'phony' datetime
+ calendar=``proleptic_gregorian``, or calendar = ``standard``
+ or ``gregorian`` and the date is after 1582-10-15).
+ Otherwise, they are 'phony' datetime
objects which support some but not all the methods of 'real' python
datetime objects. The datetime instances do not contain
a time-zone offset, even if the specified units contains one.
@@ -3472,34 +3474,44 @@
def date2num(dates,units='days since 0001-01-01 00:00:00',calendar='proleptic_gregorian'):
"""
Return numeric time values given datetime objects. The units
- of the numeric time values are described by the units argument
- and the calendar keyword. The datetime objects must
+ of the numeric time values are described by the ``units`` argument
+ and the ``calendar`` keyword. The datetime objects must
be in UTC with no time-zone offset. If there is a
time-zone offset in units, it will be applied to the
returned numeric values.
- Default behavior is the same as the matplotlib date2num function
+ Default behavior is the same as the matplotlib.dates.date2num function
but the reference time and calendar can be changed via the
- 'units' and 'calendar' keywords.
+ ``units`` and ``calendar`` keywords.
- Arguments:
+ ============== ====================================================
+ Arguments Description
+ ============== ====================================================
+ dates A datetime object or a sequence of datetime objects.
+ The datetime objects should not include a
+ time-zone offset.
+ ============== ====================================================
- dates - A datetime object or a sequence of datetime objects.
- The datetime objects should not include a time-zone offset.
+ ============== ====================================================
+ Keywords Description
+ ============== ====================================================
+ units a string of the form '<time units> since
+ <reference time>' describing the units and
+ origin of the time coordinate.
+ <time units> can be days, hours, minutes
+ or seconds. <reference time> is the time origin.
+ Default is 'days since 0001-01-01 00:00:00'.
+ calendar describes the calendar used in the time
+ calculations. All the values currently defined in
+ the CF metadata convention
+ (http://cf-pcmdi.llnl.gov/documents/cf-conventions/)
+ are supported.
+ Valid calendars ``standard``, ``gregorian``,
+ ``proleptic_gregorian``, ``noleap``, ``365_day``,
+ ``julian``, ``all_leap``, ``366_day``.
+ Default is ``proleptic_gregorian``.
+ ============== ====================================================
- units - a string of the form '<time units> since <reference time>'
- describing the time units. <time units> can be days, hours, minutes
- or seconds. <reference time> is the time origin.
- Default is 'days since 0001-01-01 00:00:00'.
-
- calendar - describes the calendar used in the time calculations.
- All the values currently defined in the CF metadata convention
- (http://cf-pcmdi.llnl.gov/documents/cf-conventions/) are supported.
- Valid calendars 'standard', 'gregorian', 'proleptic_gregorian'
- 'noleap', '365_day', '360_day', 'julian', 'all_leap', '366_day'.
- Default is 'standard'/'gregorian', which is a mixed
- Julian/Gregorian calendar. Default 'proleptic_gregorian'.
-
Returns a numeric time value, or an array of numeric time values.
The maximum resolution of the numeric time values is 1 second.
Modified: trunk/toolkits/basemap/lib/mpl_toolkits/basemap/pupynere.py
===================================================================
--- trunk/toolkits/basemap/lib/mpl_toolkits/basemap/pupynere.py 2008-06-14 16:35:55 UTC (rev 5544)
+++ trunk/toolkits/basemap/lib/mpl_toolkits/basemap/pupynere.py 2008-06-14 21:14:34 UTC (rev 5545)
@@ -37,12 +37,6 @@
from dap.client import open as open_remote
from dap.dtypes import ArrayType, GridType, typemap
-has_pynio = True
-try:
- from PyNGL import nio
-except ImportError:
- has_pynio = False
-
ABSENT = '\x00' * 8
ZERO = '\x00' * 4
NC_BYTE = '\x00\x00\x00\x01'
@@ -76,37 +70,19 @@
to be a remote OPenDAP dataset, and the python dap client is used
to retrieve the data. Only the OPenDAP Array and Grid data
types are recognized. If file does not start with 'http', it
- is assumed to be a local file. If possible, the file will be read
- with a pure python NetCDF reader, otherwise PyNIO
- (http://www.pyngl.ucar.edu/Nio.shtml) will be used (if it is installed).
- PyNIO supports NetCDF version 4, GRIB1, GRIB2, HDF4 and HDFEOS2 files.
- Data read from OPenDAP and NetCDF version 3 datasets will
+ is assumed to be a local netCDF file. Data will
automatically be converted to masked arrays if the variable has either
a 'missing_value' or '_FillValue' attribute, and some data points
are equal to the value specified by that attribute. In addition,
variables stored as integers that have the 'scale_factor' and
'add_offset' attribute will automatically be rescaled to floats when
- read. If PyNIO is used, neither of the automatic conversions will
- be performed. To suppress these automatic conversions, set the
+ read. To suppress these automatic conversions, set the
maskandscale keyword to False.
"""
if file.startswith('http'):
return _RemoteFile(file,maskandscale)
else:
- # use pynio if it is installed and the file cannot
- # be read with the pure python netCDF reader. This allows
- # netCDF version 4, GRIB1, GRIB2, HDF4 and HDFEOS files
- # to be read.
- if has_pynio:
- try:
- f = _LocalFile(file,maskandscale)
- except:
- f = nio.open_file(file)
- # otherwise, use the pupynere netCDF 3 pure python reader.
- # (will fail if file is not a netCDF version 3 file).
- else:
- f = _LocalFile(file,maskandscale)
- return f
+ return _LocalFile(file,maskandscale)
def _maskandscale(var,datout):
totalmask = zeros(datout.shape,numpy.bool)
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