swelborn · decarlof · Jan 15, 2022 · Jan 15, 2022 · Jan 15, 2022 · Jan 15, 2022
diff --git a/.gitignore b/.gitignore
@@ -120,4 +120,16 @@ dmypy.json
 *.sublime-workspace
 
 # Data folder
-data/
+data/
+
+# OS generated files 
+core
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+.spyderworkspace
+*~
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -10,16 +10,9 @@ sphinx:
   configuration: docs/conf.py
 
 conda:
-  environment: docs/environment.yml
+  environment: environment-nocuda.yml
 
 python:
   install:
     - method: pip
-      path: .
-# build:
-#   tools:
-#     python: "3.9"
-#     # You can also specify other tool versions:
-#     # nodejs: "16"
-#     # rust: "1.55"
-#     # golang: "1.17"
+      path: .
diff --git a/Untitled.ipynb b/Untitled.ipynb
@@ -0,0 +1,57 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "01ef0dd3-66df-4a9d-a98f-3041923bd1dc",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "bfeb1035c2f3458ab7ca2885266de1a3",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Dropdown(options=(('x + 0', 0), ('x + 1', 1), ('x + 2', 2), ('x + 3', 3), ('x + 4', 4), ('x + 5', 5), ('x + 6'…"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "21b32054-d63d-4a14-9f28-67bcdfc88244",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/data/ALS_832_Data/fake_als_data.h5 b/data/ALS_832_Data/fake_als_data.h5
diff --git a/data/ALS_832_Data/make_fake_als_data.py b/data/ALS_832_Data/make_fake_als_data.py
@@ -0,0 +1,106 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# In[58]:
+
+
+import numpy as np
+import h5py
+import os
+import dxchange
+
+
+# In[59]:
+
+
+filename = "./fake_als_data.h5"
+
+numslices = 100
+numrays = 120
+numangles = 80
+
+tomo = np.random.rand(numangles, numslices, numrays)
+flat = np.ones((5, numslices, numrays))  # first dimension can be changed to anything
+dark = np.zeros((5, numslices, numrays))  # first dimension can be changed to anything
+angles = np.linspace(0, np.pi, num=numangles)
+
+
+# In[60]:
+
+
+pxsize = 1  # in mm
+camera_distance = 100 * np.ones(len(tomo) + len(flat) + len(dark))  # in mm
+energy = 10000  # in eV
+
+
+# In[61]:
+
+
+if os.path.exists(filename):
+    os.remove(filename)
+with h5py.File(filename, "a") as f:
+    det = f.create_group("measurement/instrument/detector")
+    det.create_dataset("dimension_y", data=np.asarray(numslices)[np.newaxis])
+    det.create_dataset("dimension_x", data=np.asarray(numrays)[np.newaxis])
+    det.create_dataset("pixel_size", data=np.asarray(pxsize)[np.newaxis])
+    rot = f.create_group("process/acquisition/rotation")
+    rot.create_dataset("num_angles", data=np.asarray(len(angles))[np.newaxis])
+    rot.create_dataset(
+        "range",
+        data=np.asarray((180 / np.pi) * np.abs(angles[-1] - angles[0]))[np.newaxis],
+    )
+    f.create_dataset(
+        "measurement/instrument/camera_motor_stack/setup/camera_distance",
+        data=camera_distance,
+    )
+    f.create_dataset(
+        "measurement/instrument/monochromator/energy",
+        data=np.asarray(energy)[np.newaxis],
+    )
+    exch = f.create_group("exchange")
+    exch.create_dataset("data", data=tomo)
+    exch.create_dataset("data_white", data=flat)
+    exch.create_dataset("data_dark", data=dark)
+    exch.create_dataset("theta", data=(180 / np.pi) * angles)
+
+
+# In[62]:
+
+
+numslices = int(
+    dxchange.read_hdf5(filename, "/measurement/instrument/detector/dimension_y")[0]
+)
+numrays = int(
+    dxchange.read_hdf5(filename, "/measurement/instrument/detector/dimension_x")[0]
+)
+pxsize = (
+    dxchange.read_hdf5(filename, "/measurement/instrument/detector/pixel_size")[0]
+    / 10.0
+)  # /10 to convert units from mm to cm
+numangles = int(
+    dxchange.read_hdf5(filename, "/process/acquisition/rotation/num_angles")[0]
+)
+propagation_dist = dxchange.read_hdf5(
+    filename, "/measurement/instrument/camera_motor_stack/setup/camera_distance"
+)[1]
+kev = (
+    dxchange.read_hdf5(filename, "/measurement/instrument/monochromator/energy")[0]
+    / 1000
+)
+angularrange = dxchange.read_hdf5(filename, "/process/acquisition/rotation/range")[0]
+
+
+# In[63]:
+
+
+tomo, flat, dark, angles = dxchange.exchange.read_aps_tomoscan_hdf5(filename)
+print(tomo.shape, tomo.dtype, tomo.min(), tomo.max())
+print(flat.shape, flat.dtype, flat.min(), flat.max())
+print(dark.shape, dark.dtype, dark.min(), dark.max())
+print(angles.shape, angles.dtype, angles.min(), angles.max())
+
+
+# In[ ]:
+
+
+# In[ ]:
diff --git a/data/tomo77_downsampled0p5.tif → data/tiff_image/tomo77_downsampled0p5.tif b/data/tomo77_downsampled0p5.tif → data/tiff_image/tomo77_downsampled0p5.tif
diff --git a/data/tiff_sequence/tomo77_000.tiff b/data/tiff_sequence/tomo77_000.tiff
diff --git a/data/tiff_sequence/tomo77_001.tiff b/data/tiff_sequence/tomo77_001.tiff
diff --git a/data/tiff_sequence/tomo77_002.tiff b/data/tiff_sequence/tomo77_002.tiff
diff --git a/data/tiff_sequence/tomo77_003.tiff b/data/tiff_sequence/tomo77_003.tiff
diff --git a/data/tiff_sequence/tomo77_004.tiff b/data/tiff_sequence/tomo77_004.tiff
diff --git a/data/tiff_sequence/tomo77_005.tiff b/data/tiff_sequence/tomo77_005.tiff
diff --git a/data/tiff_sequence/tomo77_006.tiff b/data/tiff_sequence/tomo77_006.tiff
diff --git a/data/tiff_sequence/tomo77_007.tiff b/data/tiff_sequence/tomo77_007.tiff
diff --git a/data/tiff_sequence/tomo77_008.tiff b/data/tiff_sequence/tomo77_008.tiff
diff --git a/data/tiff_sequence/tomo77_009.tiff b/data/tiff_sequence/tomo77_009.tiff
diff --git a/data/tiff_sequence/tomo77_010.tiff b/data/tiff_sequence/tomo77_010.tiff
diff --git a/data/tiff_sequence/tomo77_011.tiff b/data/tiff_sequence/tomo77_011.tiff
diff --git a/data/tiff_sequence/tomo77_012.tiff b/data/tiff_sequence/tomo77_012.tiff
diff --git a/data/tiff_sequence/tomo77_013.tiff b/data/tiff_sequence/tomo77_013.tiff
diff --git a/data/tiff_sequence/tomo77_014.tiff b/data/tiff_sequence/tomo77_014.tiff
diff --git a/data/tiff_sequence/tomo77_015.tiff b/data/tiff_sequence/tomo77_015.tiff
diff --git a/data/tiff_sequence/tomo77_016.tiff b/data/tiff_sequence/tomo77_016.tiff
diff --git a/data/tiff_sequence/tomo77_017.tiff b/data/tiff_sequence/tomo77_017.tiff
diff --git a/data/tiff_sequence/tomo77_018.tiff b/data/tiff_sequence/tomo77_018.tiff
diff --git a/data/tiff_sequence/tomo77_019.tiff b/data/tiff_sequence/tomo77_019.tiff
diff --git a/data/tiff_sequence/tomo77_020.tiff b/data/tiff_sequence/tomo77_020.tiff
diff --git a/data/tiff_sequence/tomo77_021.tiff b/data/tiff_sequence/tomo77_021.tiff
diff --git a/data/tiff_sequence/tomo77_022.tiff b/data/tiff_sequence/tomo77_022.tiff
diff --git a/data/tiff_sequence/tomo77_023.tiff b/data/tiff_sequence/tomo77_023.tiff
diff --git a/data/tiff_sequence/tomo77_024.tiff b/data/tiff_sequence/tomo77_024.tiff
diff --git a/data/tiff_sequence/tomo77_025.tiff b/data/tiff_sequence/tomo77_025.tiff
diff --git a/data/tiff_sequence/tomo77_026.tiff b/data/tiff_sequence/tomo77_026.tiff
diff --git a/data/tiff_sequence/tomo77_027.tiff b/data/tiff_sequence/tomo77_027.tiff
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diff --git a/data/tiff_sequence/tomo77_029.tiff b/data/tiff_sequence/tomo77_029.tiff
diff --git a/data/tiff_sequence/tomo77_030.tiff b/data/tiff_sequence/tomo77_030.tiff
diff --git a/data/tiff_sequence/tomo77_031.tiff b/data/tiff_sequence/tomo77_031.tiff
diff --git a/data/tiff_sequence/tomo77_032.tiff b/data/tiff_sequence/tomo77_032.tiff
diff --git a/data/tiff_sequence/tomo77_033.tiff b/data/tiff_sequence/tomo77_033.tiff
diff --git a/data/tiff_sequence/tomo77_034.tiff b/data/tiff_sequence/tomo77_034.tiff
diff --git a/data/tiff_sequence/tomo77_035.tiff b/data/tiff_sequence/tomo77_035.tiff
diff --git a/data/tiff_sequence/tomo77_036.tiff b/data/tiff_sequence/tomo77_036.tiff
diff --git a/data/tiff_sequence/tomo77_037.tiff b/data/tiff_sequence/tomo77_037.tiff
diff --git a/data/tiff_sequence/tomo77_038.tiff b/data/tiff_sequence/tomo77_038.tiff
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diff --git a/data/tiff_sequence/tomo77_041.tiff b/data/tiff_sequence/tomo77_041.tiff
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diff --git a/data/tiff_sequence/tomo77_044.tiff b/data/tiff_sequence/tomo77_044.tiff
diff --git a/data/tiff_sequence/tomo77_045.tiff b/data/tiff_sequence/tomo77_045.tiff
diff --git a/data/tiff_sequence/tomo77_046.tiff b/data/tiff_sequence/tomo77_046.tiff
diff --git a/data/tiff_sequence/tomo77_047.tiff b/data/tiff_sequence/tomo77_047.tiff
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diff --git a/data/tiff_sequence/tomo77_049.tiff b/data/tiff_sequence/tomo77_049.tiff
diff --git a/data/tiff_sequence/tomo77_050.tiff b/data/tiff_sequence/tomo77_050.tiff
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