From fad9a599bda713aa4f35c49f8f63476e5416f8fd Mon Sep 17 00:00:00 2001
From: Lilli Freischem <lilli.freischem@physics.ox.ac.uk>
Date: Fri, 3 May 2024 10:38:31 +0000
Subject: [PATCH] miniset patching, added xrpatcher to requirements

---
 config/miniset/main.yaml           |  2 +-
 config/miniset/patch.yaml          |  8 ++++----
 config/miniset/satellite/goes.yaml | 16 ++++++++--------
 config/miniset/satellite/msg.yaml  | 16 ++++++++--------
 environments/environment_iti.yaml  |  3 ++-
 5 files changed, 23 insertions(+), 22 deletions(-)

diff --git a/config/miniset/main.yaml b/config/miniset/main.yaml
index 62330be..cc0827d 100644
--- a/config/miniset/main.yaml
+++ b/config/miniset/main.yaml
@@ -1,7 +1,7 @@
 defaults:
   - download
   - geoprocess
-  # - patch
+  - patch
   - satellite: goes
 
 stage: download
\ No newline at end of file
diff --git a/config/miniset/patch.yaml b/config/miniset/patch.yaml
index bfc1bda..e5759b6 100644
--- a/config/miniset/patch.yaml
+++ b/config/miniset/patch.yaml
@@ -1,15 +1,15 @@
 # PATH WITH GEOPROCESSED DATA
-read_path: data
+read_path: /mnt/disks/data/miniset/
 
 # PATH FOR SAVING PATCHES
-save_path: data
+save_path: /mnt/disks/data/miniset/
 
 # PATCH PARAMETERS
 patch_size: 256
 stride_size: 256
 
-# NAN CUTOFF
-nan_cutoff: 0.5
+# NAN CUTOFF: maximum allowed ratio of nan values to nonan values in a patch
+nan_cutoff: 0.1
 
 # FILETYPE TO SAVE [nc = netcdf, np = numpy]
 save_filetype: nc
diff --git a/config/miniset/satellite/goes.yaml b/config/miniset/satellite/goes.yaml
index 5420d7c..8c735a4 100644
--- a/config/miniset/satellite/goes.yaml
+++ b/config/miniset/satellite/goes.yaml
@@ -19,11 +19,11 @@ geoprocess:
 
 # preprocess:
 
-# patch:
-#   _target_: rs_tools._src.preprocessing.prepatcher.prepatch
-#   read_path: ${read_path}/goes16/geoprocessed
-#   save_path: ${save_path}/goes16/analysis
-#   patch_size: ${patch_size}
-#   stride_size: ${stride_size}
-#   nan_cutoff: ${nan_cutoff}
-#   save_filetype: ${save_filetype}
+patch:
+  _target_: rs_tools._src.preprocessing.prepatcher.prepatch
+  read_path: ${read_path}/goes16/geoprocessed
+  save_path: ${save_path}/goes16/analysis
+  patch_size: ${patch_size}
+  stride_size: ${stride_size}
+  nan_cutoff: ${nan_cutoff}
+  save_filetype: ${save_filetype}
diff --git a/config/miniset/satellite/msg.yaml b/config/miniset/satellite/msg.yaml
index 89ba2fe..4d2282b 100644
--- a/config/miniset/satellite/msg.yaml
+++ b/config/miniset/satellite/msg.yaml
@@ -19,11 +19,11 @@ geoprocess:
 
 # preprocess:
 
-# patch:
-#   _target_: rs_tools._src.preprocessing.prepatcher.prepatch
-#   read_path: ${read_path}/msg/geoprocessed
-#   save_path: ${save_path}/msg/analysis
-#   patch_size: ${patch_size}
-#   stride_size: ${stride_size}
-#   nan_cutoff: ${nan_cutoff}
-#   save_filetype: ${save_filetype}
\ No newline at end of file
+patch:
+  _target_: rs_tools._src.preprocessing.prepatcher.prepatch
+  read_path: ${read_path}/msg/geoprocessed
+  save_path: ${save_path}/msg/analysis
+  patch_size: ${patch_size}
+  stride_size: ${stride_size}
+  nan_cutoff: ${nan_cutoff}
+  save_filetype: ${save_filetype}
\ No newline at end of file
diff --git a/environments/environment_iti.yaml b/environments/environment_iti.yaml
index 751fd89..ea3a68c 100644
--- a/environments/environment_iti.yaml
+++ b/environments/environment_iti.yaml
@@ -1,4 +1,4 @@
-# name: rs_tools
+name: rs_tools_iti
 channels:
   - conda-forge
 dependencies:
@@ -62,4 +62,5 @@ dependencies:
       - hydra-core
       - hydra-zen
       - wandb
+      - xrpatcher
       
\ No newline at end of file