Remove json dependency

applications/pctdoublelut/pctdoublelut.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 import argparse
-import json
 import sys
 from multiprocessing import Pool, Manager
 import os

applications/pctpairprotons/pctpairprotons.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 import argparse
-import json
 import itk
 from itk import PCT as pct
 import numpy as np
@@ -311,8 +310,7 @@ def load_tree_as_df(root_file, tree_name):
 
     if args_info.fit is not None:  # Single LUT
         verbose("Converting energy loss or TOF to WEPL using single LUT technique…")
-        with open(args_info.fit, encoding="utf-8") as f:
-            p = json.load(f)
+        p = np.loadtxt(f)
         if args_info.fit_kind == "tof":
             xs = pairs["PreGlobalTime_out"] - pairs["PreGlobalTime_in"]
         elif args_info.fit_kind == "energy":

applications/pctweplfit/pctweplfit.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 import argparse
-import json
 import sys
 from multiprocessing import Pool, Manager
 import warnings
@@ -323,10 +322,7 @@ def fit(xs, ys, xlabel, ylabel):
                 plt.show()
 
         for d, p in ps.items():
-            with open(
-                f"{output}/{xlabel}_to_{ylabel}_fit_deg{d}.json", "w", encoding="utf-8"
-            ) as f:
-                json.dump(p, f)
+            np.savetxt(f"{output}/{xlabel}_to_{ylabel}_fit_deg{d}.txt", p)
 
     fit(tofs, wepls, "tof", "wepl")
     fit(elosses, wepls, "eloss", "wepl")

documentation/docs/wepl_calibration.md

@@ -16,7 +16,7 @@ pctweplfit \
     -v
 ```
 
-In the resulting `output` folder, along with all intermediate results (ROOT files from the GATE simulations) will be two files `eloss_to_wepl_fit_deg3.json` and `tof_to_wepl_fit_deg3.json` that contain the coefficients of the polynomials. These files can then be passed to `pctpairprotons` with the corresponding `--fit-kind` parameters.
+In the resulting `output` folder, along with all intermediate results (ROOT files from the GATE simulations) will be two files `eloss_to_wepl_fit_deg3.txt` and `tof_to_wepl_fit_deg3.txt` that contain the coefficients of the polynomials. These files can then be passed to `pctpairprotons` with the corresponding `--fit-kind` parameters.
 
 Here is an example of a `pctpairprotons` invocations with energy-loss fit:
 ```bash
@@ -26,7 +26,7 @@ pctpairprotons \
     -o pairs.mhd \
     --plane-in -110 \
     --plane-out 110 \
-    --fit output/eloss_to_wepl_fit_deg3.json \
+    --fit output/eloss_to_wepl_fit_deg3.txt \
     --fit-kind energy
 ```
 
@@ -42,7 +42,7 @@ pctdoublelut \
     -v
 ```
 
-In the resulting `output` folder, along with all intermediate results (ROOT files from the GATE simulations) will be files named `tof_coeffs_X.json` and `vel_coeffs_X.json` that contain the coefficients of the polynomials, where `X` is the polynomial degree. These files can then be passed to `pctpairprotons` with the appropriate parameters.
+In the resulting `output` folder, along with all intermediate results (ROOT files from the GATE simulations) will be files named `tof_coeffs_X.txt` and `vel_coeffs_X.txt` that contain the coefficients of the polynomials, where `X` is the polynomial degree. These files can then be passed to `pctpairprotons` with the appropriate parameters.
 
 Here is an example of a `pctpairprotons` invocations that uses the double LUT fits with polynomials of degree 9:
 ```bash
@@ -52,8 +52,8 @@ pctpairprotons \
     -o pairs.mhd \
     --plane-in -110 \
     --plane-out 110 \
-    --lut-tof output/tof_coeffs_9.json \
-    --lut-vel output/vel_coeffs_9.json \
+    --lut-tof output/tof_coeffs_9.txt \
+    --lut-vel output/vel_coeffs_9.txt \
     --quadric 1 0 1 0 0 0 0 0 0 -10000 \
     --angle 0
 ```

test/pct_application_test.py

@@ -1,4 +1,3 @@
-import json
 import pytest
 import itk
 import urllib.request
@@ -53,28 +52,26 @@ def test_weplfit_application(tmp_path):
         f"-o {output} --path-type phantom_length -d 220 -e 200 -l 220 --seed 1234 -v"
     )
 
-    with open(output / "tof_to_wepl_fit_deg3.json", encoding="utf-8") as f:
-        tof_to_wepl_fit = np.array(json.load(f))
-        reference = np.array(
-            [
-                8507.18830081492,
-                -38342.09213481464,
-                58268.25904916112,
-                -29633.875319259325,
-            ]
-        )
-        assert np.allclose(tof_to_wepl_fit, reference)
-    with open(output / "eloss_to_wepl_fit_deg3.json", encoding="utf-8") as f:
-        eloss_to_wepl_fit = np.array(json.load(f))
-        reference = np.array(
-            [
-                -5.4569381663242e-06,
-                -0.003455118013641362,
-                2.236667157315751,
-                -0.1768424416075149,
-            ]
-        )
-        assert np.allclose(eloss_to_wepl_fit, reference)
+    tof_to_wepl_fit = np.loadtxt(output / "tof_to_wepl_fit_deg3.txt")
+    reference = np.array(
+        [
+            8507.18830081492,
+            -38342.09213481464,
+            58268.25904916112,
+            -29633.875319259325,
+        ]
+    )
+    assert np.allclose(tof_to_wepl_fit, reference)
+    eloss_to_wepl_fit = np.loadtxt(output / "eloss_to_wepl_fit_deg3.txt")
+    reference = np.array(
+        [
+            -5.4569381663242e-06,
+            -0.003455118013641362,
+            2.236667157315751,
+            -0.1768424416075149,
+        ]
+    )
+    assert np.allclose(eloss_to_wepl_fit, reference)
 
 
 def test_doublelut_application(tmp_path):