cdscan xml from multiple files dropped time axis bounds --> cdutil.YEAR fails

[bhayes84]

This is on a Ubuntu 14.04.3 system with uvcdat 2.1.0.
I see the same failure on a vm with Ubuntu 13.10 with uvcdat 1.5.0-rc5.

When I used cdscan for two .nc files, the resulting xml no longer contains time axis bounds which makes the cdutil.YEAR function fail:

ev_mean = cdutil.YEAR(ev)
Traceback (most recent call last):
File "", line 1, in
File "/usr/local/uvcdat/2.1.0/lib/python2.7/site-packages/cdutil/times.py", line 1286, in get
s.append(TimeSlicer.get(self,slab,season,criteriaarg,statusbar=statusbar,sum=sum))
File "/usr/local/uvcdat/2.1.0/lib/python2.7/site-packages/cdutil/times.py", line 383, in get
slices,bounds,norm=self.slicer(tim,slicerarg)
File "/usr/local/uvcdat/2.1.0/lib/python2.7/site-packages/cdutil/times.py", line 631, in monthBasedSlicer
b0=cdtime.reltime(bnds[i][0],units)
TypeError: 'NoneType' object has no attribute 'getitem'

I am able to use cdutil.YEAR on each of the .nc files individually (and confirmed that they have bounds on their time axes).

I include output below showing the xml failure and the success on the two .nc files.
I also show the var info for the two individual .nc files.

------------ example code ----------------------------

bhayes@dge-calc:.../CESM1-CAM5/r1i1p1$ cdscan -x ev.xml evspsbl_Amon*
Finding common directory ...
Common directory:
Scanning files ...
evspsbl_Amon_CESM1-CAM5_rcp26_r1i1p1_200601-210012.nc
Setting reference time units to days since 2006-01-01 00:00:00
evspsbl_Amon_CESM1-CAM5_rcp26_r1i1p1_210101-230012.nc
Setting reference time units to days since 2006-01-01 00:00:00
ev.xml written

bhayes@dge-calc:.../CESM1-CAM5/r1i1p1$ cdat
Python 2.7.8 (default, Jan 14 2015, 10:22:34)
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.

import cdms2 as cdms
import cdutil
f = cdms.open('ev.xml')
f.variables.keys()
['time_bnds', 'lat_bnds', 'evspsbl', 'lon_bnds']
ev = f('evspsbl')
ev.shape
(3540, 192, 288)
ev_mean = cdutil.YEAR(ev)
Traceback (most recent call last):
File "", line 1, in
File "/usr/local/uvcdat/2.1.0/lib/python2.7/site-packages/cdutil/times.py", line 1286, in get
s.append(TimeSlicer.get(self,slab,season,criteriaarg,statusbar=statusbar,sum=sum))
File "/usr/local/uvcdat/2.1.0/lib/python2.7/site-packages/cdutil/times.py", line 383, in get
slices,bounds,norm=self.slicer(tim,slicerarg)
File "/usr/local/uvcdat/2.1.0/lib/python2.7/site-packages/cdutil/times.py", line 631, in monthBasedSlicer
b0=cdtime.reltime(bnds[i][0],units)
TypeError: 'NoneType' object has no attribute 'getitem'

ta = ev.getAxis(0)
ta.shape
(3540,)
tab = ta.getBounds()
type(tab)
<type 'NoneType'>

----------- mean for file 1 ---------

f1 = cdms.open('evspsbl_Amon_CESM1-CAM5_rcp26_r1i1p1_200601-210012.nc')
ev1 = f1('evspsbl')
ev1_mean = cdutil.YEAR(ev1)
ev1_mean.shape
(95, 192, 288)

f1.close()
ta1 = ev1.getAxis(0)
tab1 = ta1.getBounds()
type(tab1)
<type 'numpy.ndarray'>
tab1.shape
(1140, 2)

----------------- mean for file 2 -----

f2 = cdms.open('evspsbl_Amon_CESM1-CAM5_rcp26_r1i1p1_210101-230012.nc')
ev2 = f2('evspsbl')
ev2.shape
(2400, 192, 288)
ev2_means = cdutil.YEAR(ev2)
ev2_means.shape
(200, 192, 288)
ta2 = ev2.getAxis(0)
tab2 = ta2.getBounds()
type(tab2)
<type 'numpy.ndarray'>
tab2.shape
(2400, 2)

-------------- ev1 info ------------------

ev1.info()
*** Description of Slab evspsbl ***
id: evspsbl
shape: (1140, 192, 288)
filename:
missing_value: 1e+20
comments:
grid_name:
grid_type: generic
time_statistic:
long_name: Evaporation
units: kg m-2 s-1
comment: QFLX no change, CMIP5_table_comment: at surface; flux of water into the atmosphere due to conversion of both liquid and solid phases to vapor (from underlying surface and vegetation)
_FillValue: [ 1.00000002e+20]
autoApiInfo: <AutoAPI.AutoAPI.Info instance at 0x7efcc240ef38>
tileIndex: None
original_name: QFLX
associated_files: baseURL: http://cmip-pcmdi.llnl.gov/CMIP5/dataLocation gridspecFile: gridspec_atmos_fx_CESM1-CAM5_rcp26_r0i0p0.nc areacella: areacella_fx_CESM1-CAM5_rcp26_r0i0p0.nc
standard_name: water_evaporation_flux
cell_methods: time: mean (interval: 30 days)
cell_measures: area: areacella
original_units: kg/m2/s
history: 2012-06-08T23:37:19Z altered by CMOR: Converted units from 'kg/m2/s' to 'kg m-2 s-1'. 2012-06-08T23:37:19Z altered by CMOR: Reordered dimensions, original order: lat lon time. 2012-06-08T23:37:19Z altered by CMOR: replaced missing value flag (-1e+32) with standard missing value (1e+20).
Grid has Python id 0x7efcc241b050.
Gridtype: generic
Grid shape: (192, 288)
Order: yx
** Dimension 1 **
id: time
Designated a time axis.
units: days since 2006-01-01 00:00:00
Length: 1140
First: 15.5
Last: 34659.5
Other axis attributes:
long_name: time
standard_name: time
calendar: noleap
axis: T
Python id: 0x7efcc241b890
** Dimension 2 **
id: lat
Designated a latitude axis.
units: degrees_north
Length: 192
First: -90.0
Last: 90.0
Other axis attributes:
long_name: latitude
standard_name: latitude
axis: Y
Python id: 0x7efcc241b910
** Dimension 3 **
id: lon
Designated a longitude axis.
units: degrees_east
Length: 288
First: 0.0
Last: 358.75
Other axis attributes:
modulo: 360.0
long_name: longitude
standard_name: longitude
axis: X
topology: circular
Python id: 0x7efcc241b990
*** End of description for evspsbl ***

---------- ev2 info ---------------------

...
ev2.info()
*** Description of Slab evspsbl ***
id: evspsbl
shape: (2400, 192, 288)
filename:
missing_value: 1e+20
comments:
grid_name:
grid_type: generic
time_statistic:
long_name: Evaporation
units: kg m-2 s-1
comment: QFLX no change, CMIP5_table_comment: at surface; flux of water into the atmosphere due to conversion of both liquid and solid phases to vapor (from underlying surface and vegetation)
_FillValue: [ 1.00000002e+20]
autoApiInfo: <AutoAPI.AutoAPI.Info instance at 0x7efcc24236c8>
tileIndex: None
original_name: QFLX
associated_files: baseURL: http://cmip-pcmdi.llnl.gov/CMIP5/dataLocation gridspecFile: gridspec_atmos_fx_CESM1-CAM5_rcp26_r0i0p0.nc areacella: areacella_fx_CESM1-CAM5_rcp26_r0i0p0.nc
standard_name: water_evaporation_flux
cell_methods: time: mean (interval: 30 days)
cell_measures: area: areacella
original_units: kg/m2/s
history: 2012-06-15T22:28:22Z altered by CMOR: Converted units from 'kg/m2/s' to 'kg m-2 s-1'. 2012-06-15T22:28:22Z altered by CMOR: Reordered dimensions, original order: lat lon time. 2012-06-15T22:28:22Z altered by CMOR: replaced missing value flag (-1e+32) with standard missing value (1e+20).
Grid has Python id 0x7efcc241bf50.
Gridtype: generic
Grid shape: (192, 288)
Order: yx
** Dimension 1 **
id: time
Designated a time axis.
units: days since 2100-01-01 00:00:00
Length: 2400
First: 380.5
Last: 73349.5
Other axis attributes:
long_name: time
standard_name: time
calendar: noleap
axis: T
Python id: 0x7efcc241bf10
** Dimension 2 **
id: lat
Designated a latitude axis.
units: degrees_north
Length: 192
First: -90.0
Last: 90.0
Other axis attributes:
long_name: latitude
standard_name: latitude
axis: Y
Python id: 0x7efcc241b850
** Dimension 3 **
id: lon
Designated a longitude axis.
units: degrees_east
Length: 288
First: 0.0
Last: 358.75
Other axis attributes:
modulo: 360.0
long_name: longitude
standard_name: longitude
axis: X
topology: circular
Python id: 0x7efcc2437150
*** End of description for evspsbl ***

[doutriaux1]

confirmed in master here as well.

In the mean time please use cdutil.setTimeBoundsMonthly(ev2)

[doutriaux1]

@dnadeau4 on crunchy use:

cdscan -x charles.xml /cmip5_css02/data/cmip5/output1/NCAR/CCSM4/amip/mon/atmos/Amon/r7i1p1/evspsbl/1/*.nc