added PD modality, added code to not normalize to [0,1500]

Hendrik-code · Sep 9, 2024 · e7f1316 · e7f1316
1 parent dfb9655
commit e7f1316
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Showing 3 changed files with 15 additions and 3 deletions.
diff --git a/spineps/phase_pre.py b/spineps/phase_pre.py
@@ -14,6 +14,7 @@ def preprocess_input(
     mri_nii: NII,
     debug_data: dict,  # noqa: ARG001
     pad_size: int = 4,
+    proc_normalize_input: bool = True,
     proc_do_n4_bias_correction: bool = True,
     proc_crop_input: bool = True,
     verbose: bool = False,
@@ -24,8 +25,15 @@ def preprocess_input(
         # Crop Down
         try:
             # Enforce to range [0, 1500]
-            mri_nii.normalize_to_range_(min_value=0, max_value=9000, verbose=logger)
-            crop = mri_nii.compute_crop(dist=0) if proc_crop_input else (slice(None, None), slice(None, None), slice(None, None))
+            if proc_normalize_input:
+                mri_nii.normalize_to_range_(min_value=0, max_value=9000, verbose=logger)
+                crop = mri_nii.compute_crop(dist=0) if proc_crop_input else (slice(None, None), slice(None, None), slice(None, None))
+            else:
+                crop = (
+                    mri_nii.compute_crop(minimum=mri_nii.min(), dist=0)
+                    if proc_crop_input
+                    else (slice(None, None), slice(None, None), slice(None, None))
+                )
         except ValueError:
             logger.print("Image Nifty is empty, skip this", Log_Type.FAIL)
             return None, ErrCode.EMPTY
@@ -40,7 +48,8 @@ def preprocess_input(
             logger.print(f"N4 Bias field correction done in {perf_counter() - n4_start} sec", verbose=True)
 
         # Enforce to range [0, 1500]
-        cropped_nii.normalize_to_range_(min_value=0, max_value=1500, verbose=logger)
+        if proc_normalize_input:
+            cropped_nii.normalize_to_range_(min_value=0, max_value=1500, verbose=logger)
 
         # Uncrop again
         # uncropped_input[crop] = cropped_nii.get_array()

diff --git a/spineps/seg_enums.py b/spineps/seg_enums.py
@@ -50,6 +50,7 @@ class Modality(Enum_Compare):
     CT = auto()
     SEG = auto()
     MPR = auto()
+    PD = auto()
 
     @classmethod
     def format_keys(cls, modalities: Self | list[Self]) -> list[str]:

diff --git a/spineps/seg_run.py b/spineps/seg_run.py
@@ -255,6 +255,7 @@ def process_img_nii(  # noqa: C901
     override_postpair: bool = False,
     override_ctd: bool = False,
     proc_pad_size: int = 4,
+    proc_normalize_input: bool = True,
     # Processings
     # Semantic
     proc_sem_crop_input: bool = True,
@@ -385,6 +386,7 @@ def process_img_nii(  # noqa: C901
                 pad_size=input_package.pad_size,
                 debug_data=debug_data_run,
                 proc_crop_input=proc_sem_crop_input,
+                proc_normalize_input=proc_normalize_input,
                 proc_do_n4_bias_correction=proc_sem_n4_bias_correction,
                 verbose=verbose,
             )