Dicom extreaction and deformable reg (#59)

* type hints, deprecated get_segmentation_connected_components

* remove the word centroids in text. Remove deprecated methods

* updated registation

* readme

* merge

* make it able to run on CPU

* update has_grid

* add deformable reg

* added poi reg and tests

* update test

* updated dicom_extractor and processing tutorial

* ruff

* ruff

* update tutorial

* updated tutorial

* ruff

---------

Co-authored-by: ga84mun <robert.graf@tum.de>

.gitignore

@@ -159,4 +159,6 @@ tmp/*
 !/TPTBox/tests/sample_ct/*
 poetry.lock
 *.dcm
-*.pkl
+*.pkl
+tutorials/*PixelPandemonium/*
+tutorials/dataset-PixelPandemonium/*

TPTBox/core/bids_constants.py

@@ -25,6 +25,105 @@
     "R2star",
     "radiomics",
     "MPR",  # Rapid gradient-echo (MP RAGE) sampling
+    "IRT",
+    "MES",
+    "MEGR",
+    "MP2RAG",
+    "MPM",
+    "MT",
+    "MT",
+    "T1map",
+    "T2map",
+    "T2starmap",
+    "R1map",
+    "R2map",
+    "R2starmap",
+    "PDmap",
+    "MTRmap",
+    "MTsat",
+    "UNIT1",
+    "T1rho",
+    "MWFmap",
+    "MTVmap",
+    "Chimap",
+    "S0map",
+    "M0ma",
+    "T1w",
+    "T2w",
+    "PDw",
+    "T2starw",
+    "FLAIR",
+    "inplaneT1",
+    "inplaneT2",
+    "PDT2",
+    "angio",
+    "T2star",
+    "FLASH",
+    "VF",
+    "defacemas",
+    "dw",
+    "TB1TFL",
+    "TB1RFM",
+    "RB1CO",
+    "TB1AF",
+    "TB1DA",
+    "TB1EP",
+    "TB1SRG",
+    "TB1ma",
+    "RB1ma",
+    "ep",
+    "phase1",
+    "phase2",
+    "magnitude1",
+    "magnitude2",
+    "magnitude",
+    "fieldma",
+    "phasedif",
+    "sbre",
+    "cb",
+    "bol",
+    "as",
+    "m0sca",
+    "aslcontex",
+    "asllabelin",
+    "phas",
+    "noR",
+    "ee",
+    "iee",
+    "sti",
+    "ME",
+    "channel",
+    "coordsyste",
+    "headshap",
+    "electrode",
+    "marker",
+    "me",
+    "sti",
+    "PE",
+    "bloo",
+    "pe",
+    "event",
+    "physio",
+    "sti",
+    "TEM",
+    "SEM",
+    "uCT",
+    "BF",
+    "DF",
+    "PC",
+    "DIC",
+    "FLUO",
+    "CONF",
+    "PLI",
+    "CARS",
+    "2PE",
+    "MPE",
+    "SR",
+    "NLO",
+    "OCT",
+    "SPIM",
+    "XPC",
+    "phot",
     "stat",
     "snp",
     "log",
@@ -36,7 +135,9 @@
     "angles",
     "subvar",
     "logit",
+    "localizer",
 ]
+# https://bids-specification.readthedocs.io/en/stable/appendices/entity-table.html
 formats_relaxed = [*formats, "t2", "t1", "t2c", "t1c", "cta", "mr", "snapshot", "t1dixon", "dwi"]
 # Recommended writing style: T1c, T2c; This list is not official and can be extended.
 

TPTBox/core/bids_files.py

@@ -672,7 +672,7 @@ def get_changed_path(  # noqa: C901
         auto_add_run_id=False,
         additional_folder: str | None = None,
         dataset_path: str | None = None,
-        make_parent=True,
+        make_parent=False,
         no_sorting_mode: bool = False,
         non_strict_mode: bool = False,
     ) -> Path:
@@ -1192,9 +1192,8 @@ def filter_non_existence(
 
     def filter_dixon_only_inphase(self):
         def json_filter(x):
-            return (
-                "ImageType" not in x
-                or "W" not in x["ImageType"]
+            return "ImageType" not in x or (
+                "W" not in x["ImageType"]
                 and "F" not in x["ImageType"]
                 and "FAT" not in x["ImageType"]
                 and "WATER" not in x["ImageType"]