Skip to content

working on quality mask #7

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
gregory-halverson-jpl merged 1 commit into from
Jul 21, 2025
Merged

working on quality mask #7

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 12 additions & 0 deletions EMITL2ARFL/granule.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
from rasters import Raster, RasterGeometry

from .emit_ortho_raster import emit_ortho_raster
from .quality_mask import quality_mask

class EMITL2ARFL:
def __init__(self, directory: str):
Expand Down Expand Up @@ -32,6 +33,17 @@ def mask_filename(self) -> str:
def uncertainty_filename(self) -> str:
return glob(join(self.directory_absolute, "*_RFLUNCERT_*.nc"))[0]

def quality_mask(self, geometry: RasterGeometry) -> Raster:
raster = quality_mask(
filepath=self.mask_filename,
quality_bands=[0, 1, 2, 3, 4]
)

if geometry is not None:
raster = raster.to_geometry(geometry)

return raster

def reflectance(self, geometry: RasterGeometry) -> Raster:
raster = emit_ortho_raster(
filepath=self.reflectance_filename,
Expand Down
31 changes: 31 additions & 0 deletions EMITL2ARFL/quality_mask.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
import numpy as np
import xarray as xr

def quality_mask(filepath, quality_bands):
"""
This function builds a single layer mask to apply based on the bands selected from an EMIT L2A Mask file.

Parameters:
filepath: an EMIT L2A Mask netCDF file.
quality_bands: a list of bands (quality flags only) from the mask file that should be used in creation of mask.

Returns:
qmask: a numpy array that can be used with the emit_xarray function to apply a quality mask.
"""
# Open Dataset
mask_ds = xr.open_dataset(filepath, engine="h5netcdf")
# Open Sensor band Group
mask_parameters_ds = xr.open_dataset(
filepath, engine="h5netcdf", group="sensor_band_parameters"
)
# Print Flags used
flags_used = mask_parameters_ds["mask_bands"].data[quality_bands]
print(f"Flags used: {flags_used}")
# Check for data bands and build mask
if any(x in quality_bands for x in [5, 6]):
err_str = f"Selected flags include a data band (5 or 6) not just flag bands"
raise AttributeError(err_str)
else:
qmask = np.sum(mask_ds["mask"][:, :, quality_bands].values, axis=-1)
qmask[qmask > 1] = 1
return qmask
36 changes: 23 additions & 13 deletions Searching EMIT L2A Reflectance with earthaccess.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -22,7 +22,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -39,7 +39,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -55,7 +55,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -77,7 +77,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -121,7 +121,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -148,7 +148,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -211,7 +211,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -233,7 +233,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -253,7 +253,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -273,7 +273,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -293,7 +293,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -313,7 +313,7 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -332,6 +332,16 @@
"granule.reflectance(geometry=geometry)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"emit_mask = emit_xarray(granule.mask_filename, ortho=True)\n",
"emit_mask"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand Down