# Decoding error reading CfRadial1 file

**URL:** <https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80>\
**Category:** Data\
**Tags:** wradlib, py-art, data\
**Created:** [November 2, 2022, 8:50am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80 "2022-11-02T08:50:34Z")\
**Posts on this page:** 20\
**Page:** 1

<div class="post-metadata">

**Author:** ![adithiyrnair](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/adithiyrnair/32/84_2.png) [@adithiyrnair](https://openradar.discourse.group/u/adithiyrnair)\
**Post date:** [November 2, 2022, 8:50am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/1 "2022-11-02T08:50:34Z")

</div>

I am trying to plot CAPPI and MAX Z using wradlib. The following is the error **unable to decode time units ‘seconds since yyyy-mm-ddThh:mm:ssZ’ with “calendar ‘gregorian’”. Try opening your dataset with decode\_times=False or installing cftime if it is not installed.** After **decode\_times=False** the the reading is happening through wradlib. The Coordinates for variables are time and range . I am attaching a sample of the file that want to plot \*\*\*A notebook for ploting CAPPI and MAX is much apreciated.

The issues are

1. time unit attribute is broken
2. time\_coverage\_start is non-standard
3. time\_coverage\_end is empty
4. sweep\_start\_ray\_index/sweep stop\_ray\_index with erroneous values

Thank you

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<div class="post-metadata">

**Author:** ![kmuehlbauer](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/kmuehlbauer/32/439_2.png) [@kmuehlbauer](https://openradar.discourse.group/u/kmuehlbauer)\
**Post date:** [November 2, 2022, 8:53am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/2 "2022-11-02T08:53:17Z")

</div>

Hi @adithiyrnair,

Would be great, if you could attach the data file too.

Update: Attaching data might not work as of now. Need to check with the backend.

---

<div class="post-metadata">

**Author:** ![adithiyrnair](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/adithiyrnair/32/84_2.png) [@adithiyrnair](https://openradar.discourse.group/u/adithiyrnair)\
**Post date:** [November 2, 2022, 8:56am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/3 "2022-11-02T08:56:07Z")

</div>

> **[RCTLS\_12OCT2022\_104600\_L2B\_STD.nc](https://drive.google.com/file/d/1VtIQPmHh_YgQCfS0-htvk4pnJxWeRRPX/view?usp=share_link)**
>
> Google Drive file.

---

<div class="post-metadata">

**Author:** ![kmuehlbauer](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/kmuehlbauer/32/439_2.png) [@kmuehlbauer](https://openradar.discourse.group/u/kmuehlbauer)\
**Post date:** [November 2, 2022, 9:28am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/4 "2022-11-02T09:28:47Z")

</div>

Hi @adithiyrnair,

> [@adithiyrnair](#):
>
> 1. time unit attribute is broken
> 2. time\_coverage\_start is non-standard
> 3. time\_coverage\_end is empty
> 4. sweep\_start\_ray\_index/sweep stop\_ray\_index with erroneous values

I hope the following code snippets help to understand the issues with the file.

```python
# Just open as simple xarray.Dataset, not decoding times
vol = xr.open_dataset("RCTLS_30NOV2017_000957_L2B_STD.nc", decode_times=False)

# 1./2. fix time unit and time_coverage_start
start_time = "".join(vol.time_coverage_start.astype(str).values)
start_time = dt.datetime.strptime(start_time, "%Y-%m-%dT%H:%M:%SZ")
vol["time_coverage_start"] = start_time
# time-units is wrong: "seconds since yyyy-mm-ddThh:mm:ssZ"
vol["time"].attrs["units"] = f"seconds since {start_time}"
# new correct value: "seconds since 2017-11-30 00:09:57"
# now we can decode time (!)
vol = xr.decode_cf(vol)

# 4. fix ray_index
# we have wrong values here, so that we cannot extract the individual sweeps
# sweep_start_ray_index: array([0, 0, 0], dtype=int32)
# sweep_end_ray_index: array([0, 0, 0], dtype=int32)

# to resolve this we identify these indices with the help of elevation
# get unique elevations (removing "0" in this case, as it is not an elevation)
ele = sorted(list(set(vol.elevation.values) ^ {0}))
vele = vol.elevation
sweep_start_ray_index = [vele.where(vele==el).argmin("time").values.item() for el in ele]
sweep_end_ray_index = [vol.dims["time"] - vele.where(vele==el)[::-1].argmin("time").values.item() for el in ele]
vol["sweep_start_ray_index"].values = sweep_start_ray_index
vol["sweep_end_ray_index"].values = sweep_end_ray_index

# assign data to wradlib RadarVolume()
# now we have everything in place and can extract individual sweeps
# this is done via private functions of wradlib, so take with care
sweeps = [wrl.io.xarray._assign_data_radial(vol, sweep=f"sweep_{i+1}")[0] for i in range(vol.dims["sweep"])]
new_vol = wrl.io.RadarVolume(engine="cfradial1")
new_vol.extend(sweeps)
new_vol.sort(key=lambda x: x.time.min().values)

# write to CfRadial2-like file (which can be read by new package https://github.com/openradar/xradar)
new_vol.to_cfradial2("test_cfradial2.nc")

```

After that you can interpolate your data into a 3D-grid and plot MAX CAPPI like:

```auto
# Iterate over sweeps and process
swp_list = []
for v in new_vol:
    # georeference and stack dimensions
    swp = v.pipe(wrl.georef.georeference_dataset).stack(points=["azimuth", "range"])
    swp_list.append(swp)

# concat sweeps to volume
vol0 = xr.concat(swp_list, dim="points")

# Create XYZ Coordinate DataArray
xyz = xr.concat([vol0.x, vol0.y, vol0.z], dim="xyz").transpose()

# Create Target 3D Grid, choose your wanted resolution
xcnt = 100
ycnt = 100
zcnt = 200
trgx = np.linspace(xyz[:, 0].min(),xyz[:, 0].max(), xcnt)
trgy = np.linspace(xyz[:, 1].min(),xyz[:, 1].max(), ycnt)
trgz = np.linspace(0, 20000, zcnt)
yy, hh, xx = np.meshgrid(trgy,trgz,trgx)
trgxyz = np.stack([xx.flatten(), yy.flatten(), hh.flatten()]).T

# Create Gridder/Interpolator
trgshape=xx.shape
gridder = wrl.vpr.CAPPI(polcoords=xyz,
                        gridcoords=trgxyz,
                        gridshape=trgshape,
                        maxrange=200000,
                        minelev=0,
                        maxelev=90,
                        ipclass=wrl.ipol.Nearest)

# Interpolate Data into 3D Grid
crtd_ref = vol0.DBZ
vol_zh = np.ma.masked_invalid(gridder(crtd_ref.values).reshape(trgshape))

trgx = trgxyz[:, 0].reshape(trgshape)[0, 0, :]
trgy = trgxyz[:, 1].reshape(trgshape)[0, :, 0]
trgz = trgxyz[:, 2].reshape(trgshape)[:, 0, 0]
yy, hh, xx = np.meshgrid(trgy,trgz,trgx)

# Plot MAXCAPPI
wrl.vis.plot_max_plan_and_vert(trgx, trgy, trgz, vol_zh, unit="dBZH",
cmap="jet", levels=range(-10, 60))

```

You would have to tweak the plot as needed.

You also might have a look at @syedhamidali’s nice package [syedhamidali/PyScanCf: 1.0.21](https://zenodo.org/record/7136453) which is based on Py-ART and dedicated to IMD radars.

HTH,  
Kai

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<div class="post-metadata">

**Author:** ![adithiyrnair](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/adithiyrnair/32/84_2.png) [@adithiyrnair](https://openradar.discourse.group/u/adithiyrnair)\
**Post date:** [November 2, 2022, 9:30am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/5 "2022-11-02T09:30:42Z")

</div>

Thank you Kai

Let me check it

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<div class="post-metadata">

**Author:** ![adithiyrnair](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/adithiyrnair/32/84_2.png) [@adithiyrnair](https://openradar.discourse.group/u/adithiyrnair)\
**Post date:** [November 2, 2022, 10:49am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/6 "2022-11-02T10:49:29Z")

</div>

start\_time = “”.join(vol.time\_coverage\_start.astype(str).values)  
error in this line showing

error : **can only join an iterable**

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<div class="post-metadata">

**Author:** ![kmuehlbauer](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/kmuehlbauer/32/439_2.png) [@kmuehlbauer](https://openradar.discourse.group/u/kmuehlbauer)\
**Post date:** [November 2, 2022, 10:57am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/7 "2022-11-02T10:57:55Z")

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@adithiyrnair Unfortunately I can’t reproduce this error with either of your two files.

The error message means, that `vol.time_coverage_start.astype(str).values` is not iterable (eg. a scalar and not a list/array). Can you print the content?

```python
print(vol.time_coverage_start.astype(str).values)

```

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<div class="post-metadata">

**Author:** ![adithiyrnair](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/adithiyrnair/32/84_2.png) [@adithiyrnair](https://openradar.discourse.group/u/adithiyrnair)\
**Post date:** [November 2, 2022, 10:59am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/8 "2022-11-02T10:59:15Z")

</div>

this is the output

2017-11-30T00:01:00Z

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<div class="post-metadata">

**Author:** ![kmuehlbauer](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/kmuehlbauer/32/439_2.png) [@kmuehlbauer](https://openradar.discourse.group/u/kmuehlbauer)\
**Post date:** [November 2, 2022, 11:01am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/9 "2022-11-02T11:01:25Z")

</div>

This value is already correct. So this means in that case no correction is needed. Did you by chance run that particular code block twice?

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<div class="post-metadata">

**Author:** ![adithiyrnair](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/adithiyrnair/32/84_2.png) [@adithiyrnair](https://openradar.discourse.group/u/adithiyrnair)\
**Post date:** [November 2, 2022, 11:02am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/10 "2022-11-02T11:02:07Z")

</div>

Yeah by accident… Anyway thank you

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<div class="post-metadata">

**Author:** ![adithiyrnair](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/adithiyrnair/32/84_2.png) [@adithiyrnair](https://openradar.discourse.group/u/adithiyrnair)\
**Post date:** [November 2, 2022, 11:08am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/11 "2022-11-02T11:08:02Z")

</div>

new\_vol.to\_cfradial2(“test.nc”)

error: unsupported dtype for netCDF4 variable: datetime64[ns]

any help

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<div class="post-metadata">

**Author:** ![kmuehlbauer](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/kmuehlbauer/32/439_2.png) [@kmuehlbauer](https://openradar.discourse.group/u/kmuehlbauer)\
**Post date:** [November 2, 2022, 11:13am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/12 "2022-11-02T11:13:43Z")

</div>

Please send the output of `wrl.show_versions()`. This smells like dependency issue.

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<div class="post-metadata">

**Author:** ![adithiyrnair](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/adithiyrnair/32/84_2.png) [@adithiyrnair](https://openradar.discourse.group/u/adithiyrnair)\
**Post date:** [November 2, 2022, 11:15am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/13 "2022-11-02T11:15:37Z")

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## INSTALLED VERSIONS

commit: None  
python: 3.8.13 (default, Oct 21 2022, 23:50:54)  
[GCC 11.2.0]  
python-bits: 64  
OS: Linux  
OS-release: 5.15.0-52-generic  
machine: x86\_64  
processor: x86\_64  
byteorder: little  
LC\_ALL: None  
LANG: en\_IN  
LOCALE: (‘en\_IN’, ‘ISO8859-1’)  
libhdf5: 1.10.6  
libnetcdf: 4.8.1

xarray: 0.20.1  
pandas: 1.4.4  
numpy: 1.23.3  
scipy: 1.9.1  
netCDF4: 1.5.7  
pydap: None  
h5netcdf: 1.0.2  
h5py: 3.1.0  
Nio: None  
zarr: None  
cftime: 1.5.1.1  
nc\_time\_axis: None  
PseudoNetCDF: None  
rasterio: None  
cfgrib: None  
iris: None  
bottleneck: 1.3.5  
dask: None  
distributed: None  
matplotlib: 3.1.3  
cartopy: 0.18.0  
seaborn: None  
numbagg: None  
fsspec: None  
cupy: None  
pint: None  
sparse: None  
setuptools: 65.5.0  
pip: 22.2.2  
conda: None  
pytest: None  
IPython: 8.4.0  
sphinx: None

wradlib: 1.17.0

---

<div class="post-metadata">

**Author:** ![kmuehlbauer](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/kmuehlbauer/32/439_2.png) [@kmuehlbauer](https://openradar.discourse.group/u/kmuehlbauer)\
**Post date:** [November 2, 2022, 11:21am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/14 "2022-11-02T11:21:43Z")

</div>

Please update “xarray” (I have xarray: 2022.10.0). Also consider to install `nc_time_axis`, which might bring in some convenience code support for xarray/netCDF4.

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<div class="post-metadata">

**Author:** ![adithiyrnair](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/adithiyrnair/32/84_2.png) [@adithiyrnair](https://openradar.discourse.group/u/adithiyrnair)\
**Post date:** [November 2, 2022, 11:30am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/15 "2022-11-02T11:30:44Z")

</div>

yes it worked. Thanks again

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<div class="post-metadata">

**Author:** ![adithiyrnair](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/adithiyrnair/32/84_2.png) [@adithiyrnair](https://openradar.discourse.group/u/adithiyrnair)\
**Post date:** [November 2, 2022, 1:07pm UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/16 "2022-11-02T13:07:44Z")

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AttributeError: Module ‘osgeo.osr’ is not installed.

You tried to access function/module/attribute ‘SpatialReference’  
from module ‘osgeo.osr’.  
This module is optional right now in wradlib.  
You need to separately install this dependency.  
Please refer to [Installation — wradlib](https://docs.wradlib.org/en/stable/installation.html#optional-dependencies)  
for further instructions.

I already installed GDAL. Do i need to seperately install, I am Using Conda… Where can i download that perticular package. In conda site the package is in the name of GDAL

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<div class="post-metadata">

**Author:** ![kmuehlbauer](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/kmuehlbauer/32/439_2.png) [@kmuehlbauer](https://openradar.discourse.group/u/kmuehlbauer)\
**Post date:** [November 2, 2022, 1:21pm UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/17 "2022-11-02T13:21:07Z")

</div>

GDAL is correct and this should work if GDAL is installed.

But are you sure you are working inside a conda environment? Your above output doesn’t mention conda.

> [@adithiyrnair](#):
>
> python: 3.8.13 (default, Oct 21 2022, 23:50:54)  
> [GCC 11.2.0]

> [@adithiyrnair](#):
>
> conda: None

---

<div class="post-metadata">

**Author:** ![adithiyrnair](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/adithiyrnair/32/84_2.png) [@adithiyrnair](https://openradar.discourse.group/u/adithiyrnair)\
**Post date:** [November 2, 2022, 1:28pm UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/18 "2022-11-02T13:28:01Z")

</div>

But i am actually running in conda, I created a new enviroment only for wradlib in anaconda…and from that i am using

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<div class="post-metadata">

**Author:** ![kmuehlbauer](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/kmuehlbauer/32/439_2.png) [@kmuehlbauer](https://openradar.discourse.group/u/kmuehlbauer)\
**Post date:** [November 2, 2022, 1:34pm UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/19 "2022-11-02T13:34:04Z")

</div>

Are you running the code via jupyter lab/notebook? The environment might be missing the jupyter kernel. For a quick verification just install jupyterlab inside your wradlib environment. Make sure to activate your environment and start lab from there.

```bash
(base) $ conda activate wradlib
(wradlib) $ conda install jupyterlab
(wradlib) $ conda list
(wradlib) $ jupyter lab

```

---

<div class="post-metadata">

**Author:** ![adithiyrnair](https://yyz2.discourse-cdn.com/free1/user_avatar/openradar.discourse.group/adithiyrnair/32/84_2.png) [@adithiyrnair](https://openradar.discourse.group/u/adithiyrnair)\
**Post date:** [November 3, 2022, 10:05am UTC](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80/20 "2022-11-03T10:05:41Z")

</div>

hi @kmuehlbauer  
The problem got solved after upgrading numpy. I found from stack overflow that installing Gdal will actually downgrade the numpoy version. so after installlation of Gdal we have to upgrade numpy to work OSgeo.osr properly.

I couldn’t replay to you yesterday because of chat limit shown by the site 😆

[Next page](https://openradar.discourse.group/t/decoding-error-reading-cfradial1-file/80.md?page=2)