From a4aa179ea5daaccfe52db87fefc6472b2dc490a0 Mon Sep 17 00:00:00 2001
From: Gregory Halverson <gregory.halverson@gmail.com>
Date: Tue, 17 Jun 2025 15:41:57 -0700
Subject: [PATCH] working on quality mask

---
 EMITL2ARFL/granule.py                         | 12 +++++++
 EMITL2ARFL/quality_mask.py                    | 31 ++++++++++++++++
 ...MIT L2A Reflectance with earthaccess.ipynb | 36 ++++++++++++-------
 3 files changed, 66 insertions(+), 13 deletions(-)
 create mode 100644 EMITL2ARFL/quality_mask.py

diff --git a/EMITL2ARFL/granule.py b/EMITL2ARFL/granule.py
index 13ad108..a6e3e13 100644
--- a/EMITL2ARFL/granule.py
+++ b/EMITL2ARFL/granule.py
@@ -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):
@@ -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,
diff --git a/EMITL2ARFL/quality_mask.py b/EMITL2ARFL/quality_mask.py
new file mode 100644
index 0000000..0c13504
--- /dev/null
+++ b/EMITL2ARFL/quality_mask.py
@@ -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
\ No newline at end of file
diff --git a/Searching EMIT L2A Reflectance with earthaccess.ipynb b/Searching EMIT L2A Reflectance with earthaccess.ipynb
index 10a09a6..e8d64e8 100644
--- a/Searching EMIT L2A Reflectance with earthaccess.ipynb	
+++ b/Searching EMIT L2A Reflectance with earthaccess.ipynb	
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -22,7 +22,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -39,7 +39,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -77,7 +77,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -121,7 +121,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -148,7 +148,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -211,7 +211,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -233,7 +233,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -253,7 +253,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -273,7 +273,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -293,7 +293,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -313,7 +313,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -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,