From 19a108f7d65580e1ba5b039afb9f126c5f850c0f Mon Sep 17 00:00:00 2001
From: acolite <quinten.vanhellemont@naturalsciences.be>
Date: Thu, 25 Jul 2024 15:57:03 +0200
Subject: [PATCH 1/2] Switch to openpyxl

---
 environment.yml            |  4 ++--
 polymer/level1_landsat8.py | 24 +++++++++++-------------
 polymer/params.py          | 23 ++++++++++-------------
 3 files changed, 23 insertions(+), 28 deletions(-)

diff --git a/environment.yml b/environment.yml
index c678214..74b0020 100644
--- a/environment.yml
+++ b/environment.yml
@@ -28,7 +28,7 @@ dependencies:
   - bioconda::ecmwfapi
 
   # for Landsat8:
-  - xlrd<2
+  - openpyxl
 
   # For Sentinel-2:
   - glymur
@@ -42,4 +42,4 @@ dependencies:
   - pytest
   - pytest-html
   - pytest-xdist
-  - matplotlib
\ No newline at end of file
+  - matplotlib
diff --git a/polymer/level1_landsat8.py b/polymer/level1_landsat8.py
index bd9559c..674f384 100755
--- a/polymer/level1_landsat8.py
+++ b/polymer/level1_landsat8.py
@@ -16,7 +16,9 @@
 import numpy as np
 import os
 from os.path import dirname, join
-import xlrd
+
+# QV 2024-07-25 use openpyxl instead of xlrd
+from openpyxl import load_workbook
 
 gdal_major_version = int(osgeo.__version__.split('.')[0])
 
@@ -206,9 +208,7 @@ def init_meta(self):
     def init_spectral(self):
         dir_aux_oli = join(dirname(dirname(__file__)), 'auxdata', 'oli')
         srf_file = join(dir_aux_oli, 'Ball_BA_RSR.v1.2.xlsx')
-
-        wb = xlrd.open_workbook(srf_file)
-
+        wb = load_workbook(filename = srf_file)
 
         self.wav = OrderedDict()
         for b, bname in [(440, 'CoastalAerosol'),
@@ -218,18 +218,16 @@ def init_spectral(self):
                          (865, 'NIR'),
                          (1610, 'SWIR1'),
                          (2200, 'SWIR2')]:
-            sh = wb.sheet_by_name(bname)
+            sh = wb[bname]
 
             wav, srf = [], []
-
-            i=0
-            while True:
+            i=1
+            while i<wb[bname].max_row:
                 i += 1
-                try:
-                    wav.append(sh.cell(i, 0).value)
-                    srf.append(sh.cell(i, 1).value)
-                except IndexError:
-                    break
+                if sh.cell(i, 1).value is None: break
+                wav.append(sh.cell(i, 1).value)
+                srf.append(sh.cell(i, 2).value)
+
 
             wav, srf = np.array(wav), np.array(srf)
             wav_eq = np.trapz(wav*srf)/np.trapz(srf)
diff --git a/polymer/params.py b/polymer/params.py
index 788f673..68bf640 100644
--- a/polymer/params.py
+++ b/polymer/params.py
@@ -721,7 +721,7 @@ def defaults_hico(self):
         self.K_NO2 = K_NO2_HICO
 
         self.band_cloudmask = 862
-    
+
 
     def defaults_prisma(self):
         self.bands_corr = [
@@ -753,7 +753,8 @@ def defaults_oli(self):
         '''
         Landsat8/OLI defaults
         '''
-        import xlrd
+        # QV 2024-07-25 use openpyxl instead of xlrd
+        from openpyxl import load_workbook
         import pandas as pd
 
         self.bands_corr = [440, 480, 560, 655, 865      ]
@@ -775,7 +776,7 @@ def defaults_oli(self):
         self.K_OZ = OrderedDict()
         srf_file = join(self.dir_base, 'auxdata', 'oli',
                         'Ball_BA_RSR.v1.2.xlsx')
-        wb = xlrd.open_workbook(srf_file)
+        wb = load_workbook(filename = srf_file)
 
         solar_spectrum_file = join(self.dir_common, 'SOLAR_SPECTRUM_WMO_86')
         solar_data = pd.read_csv(solar_spectrum_file, sep=' ')
@@ -793,18 +794,16 @@ def defaults_oli(self):
                          (865, 'NIR'),
                          (1610, 'SWIR1'),
                          (2200, 'SWIR2')]:
-            sh = wb.sheet_by_name(bname)
+            sh = wb[bname]
 
             wav, srf = [], []
 
-            i=0
-            while True:
+            i=1
+            while i<wb[bname].max_row:
                 i += 1
-                try:
-                    wav.append(sh.cell(i, 0).value)
-                    srf.append(sh.cell(i, 1).value)
-                except IndexError:
-                    break
+                if sh.cell(i, 1).value is None: break
+                wav.append(sh.cell(i, 1).value)
+                srf.append(sh.cell(i, 2).value)
 
             wav, srf = np.array(wav), np.array(srf)
 
@@ -892,5 +891,3 @@ def finalize(self):
 
         # number of terms in the model
         self.Ncoef = self.atm_model.count(',')+1
-
-

From ff5337172b6ba97671a4a6f91e8ab97b006b0208 Mon Sep 17 00:00:00 2001
From: acolite <quinten.vanhellemont@naturalsciences.be>
Date: Thu, 25 Jul 2024 16:23:31 +0200
Subject: [PATCH 2/2] Add numpy<2

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index 74b0020..b8b0f60 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,6 +7,7 @@ channels:
   - defaults
 dependencies:
   - python
+  - numpy<2
   - scipy
   - xarray
   - cython