From 72693c6cca58ba5f17cbe072765978020b794c7a Mon Sep 17 00:00:00 2001
From: Christian C <cc@localhost>
Date: Tue, 27 Jan 2026 19:19:59 -0800
Subject: Simplification

---
 .gitignore     |  6 ++++++
 README.md      | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++++++----
 buildall.sh    | 29 +++++++++++++++++++++++++++
 load_c_data.py | 27 +++++++++++++++++++++++++
 run.sh         |  4 ----
 5 files changed, 121 insertions(+), 8 deletions(-)
 create mode 100755 buildall.sh
 create mode 100755 load_c_data.py
 delete mode 100755 run.sh

diff --git a/.gitignore b/.gitignore
index 9ef52ff..8284f6b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,12 @@
 # Build files
 build/
 
+# Virtual Environment
+.venv/
+
 # Data files
 data/
 output/
+# pixi environments
+.pixi/*
+!.pixi/config.toml
diff --git a/README.md b/README.md
index 2c56d27..f10e8d2 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,65 @@
 ** Example Usage
 
-```sh
-for file in data/HT-*/; do ./run.sh `basename $file`; done
+For the following labelling input structure
+```
+data/
+├── test
+│   ├── HT-A1
+│   │   ├── Label1.tif
+│   │   ├── OtherLabel.tif
+│   │   ├── NameMe.tif
+│   │   └── A1.labels.tif[4].tif
+│   └── HT-A2
+│       ├── Label.tif
+│       ├── 2.tif
+│       └── A2.tif
+└── train
+    ├── HT-B1
+    │   └── B1.labels.tif[0].tif
+    ├── HT-B2
+    │   ├── B2.tif\ [1].tif
+    │   ├── B2.tif\ [2].tif
+    │   └── B2.tif\ [3].tif
+    ├── HT-C5
+    │   ├── C5.tif\ [1].tif
+    │   ├── C5.tif\ [2].tif
+    │   └── C5.tif\ [3].tif
+    └── HT-J9
+        └── J9.tif[1].tif
 ```
 
+Simply run:
 ```sh
-mkdir -p output/small/
-./build/prog sample_data/small output/small/small.bin output/small/small.png
+./buildall.sh
+```
+
+To get:
+```
+output/
+├── test
+│   ├── HT-A1.bin
+│   ├── HT-A1.png
+│   ├── HT-A1_seg.npy
+│   ├── HT-A1.tif
+│   ├── HT-A2.bin
+│   ├── HT-A2.png
+│   ├── HT-A2_seg.npy
+│   └── HT-A2.tif
+└── train
+    ├── HT-B1.bin
+    ├── HT-B1.png
+    ├── HT-B1_seg.npy
+    ├── HT-B1.tif
+    ├── HT-B2.bin
+    ├── HT-B2.png
+    ├── HT-B2_seg.npy
+    ├── HT-B2.tif
+    ├── HT-C5.bin
+    ├── HT-C5.png
+    ├── HT-C5_seg.npy
+    ├── HT-C5.tif
+    ├── HT-J9.bin
+    ├── HT-J9.png
+    ├── HT-J9_seg.npy
+    └── HT-J9.tif
 ```
diff --git a/buildall.sh b/buildall.sh
new file mode 100755
index 0000000..7cccd23
--- /dev/null
+++ b/buildall.sh
@@ -0,0 +1,29 @@
+#!/bin/sh
+make
+
+CLEAN="t"
+
+builder() {
+	SOURCE="$1"
+	SNAME="`basename \"${SOURCE}\"`"
+	DNAME="`dirname \"${SOURCE}\"`"
+	mkdir -p ../output/${DNAME}
+	../build/prog -s -n 8 -d ${SOURCE} -b ../output/${DNAME}/${SNAME}.bin -p ../output/${DNAME}/${SNAME}.png
+}
+
+cd data/
+for dname in */*; do
+	builder "${dname}" &
+done
+wait
+
+cd ..
+for bname in output/*/*.bin; do
+	python load_c_data.py "${bname}" &
+done
+wait
+
+if [ "${CLEAN}" = "t" ]; then
+	rm output/*/*.bin
+	rm output/*/*.png
+fi
diff --git a/load_c_data.py b/load_c_data.py
new file mode 100755
index 0000000..a3a905b
--- /dev/null
+++ b/load_c_data.py
@@ -0,0 +1,27 @@
+#!/usr/bin/env python3.11
+import numpy as np
+from sys import argv
+from matplotlib import pyplot as plt
+import tifffile
+#from tqdm.std import tqdm
+
+FILE_NAME=None
+if len(argv) > 1:
+    FILE_NAME = argv[1]
+DTYPE=np.uint16
+WIDTH,HEIGHT=1920,2560
+data = np.fromfile(FILE_NAME, dtype=DTYPE)
+_im = plt.imread(FILE_NAME[:-len("bin")] + "png")
+w,h,c = _im.shape
+if w <= 4:
+    c,w,h = w,h,c
+WIDTH,HEIGHT = w,h
+labels = data.reshape(WIDTH,HEIGHT)
+
+BASE="/home/physics/cunnichr/Data/HistologyArrays/HistologyArray00/"
+NAME = FILE_NAME[-len("HT-XX.bin"):-len(".bin")]
+image = plt.imread(BASE + NAME + "/image.png")
+print(FILE_NAME[:-len("bin")] + "tif", "\n", image.transpose(2,0,1).shape, len(np.unique(labels)))
+tifffile.imwrite(FILE_NAME[:-len("bin")] + "tif", image.transpose(2,0,1)[:3,...])
+#np.savez(FILE_NAME[:-len("bin")] + ".npz", image=[], masks=labels)
+np.save(FILE_NAME[:-len(".bin")] + "_seg.npy", dict(image=image, masks=labels))
diff --git a/run.sh b/run.sh
deleted file mode 100755
index 8b9c597..0000000
--- a/run.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-SOURCE="$1"
-mkdir -p output/${SOURCE}
-./build/prog -s -n 8 -d data/${SOURCE} -b output/${SOURCE}/${SOURCE}.bin -p output/${SOURCE}/${SOURCE}.png
-- 
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