Merge pull request #31 from Bradley-Karat/patch-1

Update get_phase_encode_txt.py

Adding support for different vendors json naming conventions (ex. PhaseEncodingDirection vs. PhaseEncodingAxis)

And EstimatedEffectiveEchoSpacing

Note that the PhaseEncodingAxis tag in the json file never includes the direction (ie is just i,j,k, never with a '-' in front). So for rev phase encoded acquisitions would still need to find the direction some other way..

snakedwi/workflow/scripts/get_phase_encode_txt.py

@@ -2,7 +2,6 @@
 import json
 import numpy as np
 
-
 # load nifti
 bzero = nib.load(snakemake.input.bzero_nii)
 
@@ -15,8 +14,13 @@
 
 imsize = np.array(bzero.header.get_data_shape())
 
-phenc_axis = json_dwi["PhaseEncodingDirection"][0]  # either i, j, k
-
+if "PhaseEncodingDirection" in json_dwi:
+	phenc_axis = json_dwi["PhaseEncodingDirection"][0] 
+	phenc_string = "PhaseEncodingDirection"
+elif "PhaseEncodingAxis" in json_dwi:
+	phenc_axis = json_dwi["PhaseEncodingAxis"][0]  # either i, j, k
+	phenc_string = "PhaseEncodingAxis"
+
 if phenc_axis == "i":
     vec = np.array([1, 0, 0])
 elif phenc_axis == "j":
@@ -25,28 +29,34 @@
     vec = np.array([0, 0, 1])
 
 # print(f'vec: {vec}')
-# print(f'imsize: {imsize}')
+# print(f'imsize: {imsize}')f
 
 numPhaseEncodes = imsize[np.where(vec > 0)]
 
 # print(f'numPhaseEncodes: {numPhaseEncodes}')
 
 # check for i-, j-, k-; flip to -1 if so..
-if len(json_dwi["PhaseEncodingDirection"]) == 2:
-    if json_dwi["PhaseEncodingDirection"][1] == "-":
+if len(json_dwi[phenc_string]) == 2:
+    if json_dwi[phenc_string][1] == "-":
         vec[np.where(vec > 0)] = -1
 
-if not "EffectiveEchoSpacing" in json_dwi:
+if "EffectiveEchoSpacing" in json_dwi:
+    phenc_line = np.hstack(
+        [vec, np.array(json_dwi["EffectiveEchoSpacing"] * numPhaseEncodes)]
+    )
+elif "EstimatedEffectiveEchoSpacing" in json_dwi:
+    print("Estimtated Effective Echo Spacing found, using that")
+    phenc_line = np.hstack(
+        [vec, np.array(json_dwi["EstimatedEffectiveEchoSpacing"] * numPhaseEncodes)]
+    )   
+else:
     print("EffectiveEchoSpacing not defined in JSON, using default value")
-    json_dwi["EffectiveEchoSpacing"] = snakemake.config[
-        "default_effective_echo_spacing"
-    ]
-
+    json_dwi["EffectiveEchoSpacing"] = snakemake.config["default_effective_echo_spacing"]
+
 # create the phenc_line row
-phenc_line = np.hstack(
-    [vec, np.array(json_dwi["EffectiveEchoSpacing"] * numPhaseEncodes)]
-)
-
+#phenc_line = np.hstack(
+#    [vec, np.array(json_dwi["EffectiveEchoSpacing"] * numPhaseEncodes)]
+#)
 
 # replicate to the number of volumes, if it is 4d
 if len(imsize) == 4: