add basic code for fcsv reader

niftynet/contrib/fcsv_reader/0001_27588.fcsv

@@ -0,0 +1,59 @@
+#Fiducial List file /Shared/sinapse/CACHE/20160520_PREDICTHD_long_CACHE/singleSession_0001_27588/LandmarkInitialize/BCD/BCD_ACPC_Landmarks.fcsv
+#numPoints = 51
+#symbolScale = 5
+#visibility = 1
+#textScale = 4.5
+#color = 0.4,1,1
+#selectedColor = 1,0.5,0.5
+#label,x,y,z,sel,vis
+AC,0.022481131635158524,-0.03241262513099352,0.09632827194379834,1,1
+BPons,1.8645660536814521,-28.501591695014845,-35.49375715884035,1,1
+CM,-0.1028433173519987,-17.642400076852653,-2.0585982670143674,1,1
+LE,-27.641465753788214,47.75605605907536,-21.70617976413726,1,1
+PC,-0.2108937917773761,-27.104980286166697,-0.1350388791656596,1,1
+RE,30.559804523104255,48.13686574145882,-20.777926893461615,1,1
+RP,0.13298449434801518,-23.344233553271124,-12.918515104144294,1,1
+RP_front,-0.24335804895573276,-34.74426147003849,-18.010587594162608,1,1
+SMV,0.2901110429337945,-39.01916051821165,-16.479360968313156,1,1
+VN4,1.2135580596967876,-48.61438937833321,-25.39944497043434,1,1
+callosum_left,-23.375289609464307,-55.032609759616484,11.91376001508971,1,1
+callosum_right,26.024619245872778,-49.85979642522741,13.384298874091428,1,1
+dens_axis,-0.8785573145930912,-27.72734874384416,-66.43535070699247,1,1
+genu,-0.19267442277729407,16.852151782196323,9.601355986645792,1,1
+l_caud_head,-14.826197445878034,14.969179678294092,6.621049135823253,1,1
+l_corp,-29.41408681040191,-48.08223522160287,-35.84205560284369,1,1
+l_front_pole,-10.43080329908726,53.17084799531153,28.029902923214014,1,1
+l_inner_corpus,-1.577055722348477,-18.73735188137699,21.111148623406653,1,1
+l_lat_ext,-61.33259693564417,-40.82308140324586,-4.190516289985421,1,1
+l_occ_pole,-8.935637969528843,-102.65878573571989,-5.837500696266878,1,1
+l_prim_ext,-29.229301824503622,-41.177713640738396,-24.48296961332181,1,1
+l_sup_ext,-16.78424200280258,-27.884110195471298,64.88238176551914,1,1
+l_temp_pole,-35.32176500340664,20.234703805307532,-20.679701169791695,1,1
+lat_left,-19.569717830135655,-13.826314317041977,-11.93342179066418,1,1
+lat_right,21.750967645794635,-12.62486750210986,-12.367617913060382,1,1
+lat_ven_left,-31.83448634749371,-14.58677502396956,-14.590460937133567,1,1
+lat_ven_right,31.013344442138603,-9.716829769729676,-16.036374148067793,1,1
+left_cereb,-10.160748762541349,-38.73963194154938,-23.529387845641356,1,1
+left_lateral_inner_ear,-56.986813502594565,-8.999555826614252,-41.7096273934753,1,1
+m_ax_inf,0.12493164264197165,-48.06859796822409,12.876122467230502,1,1
+m_ax_sup,-0.7682506235437605,6.482718224432941,23.69425242882713,1,1
+mid_basel,-0.6797813996851534,-11.600530018222955,4.892343363773401,1,1
+mid_lat,-0.01344360923866994,-15.238393913447926,-5.3850638051877056,1,1
+mid_prim_inf,0.6582819816529446,-51.7019178660373,-24.701056882328267,1,1
+mid_prim_sup,0.30715640203901096,-65.72438089175131,-9.043731532799985,1,1
+mid_sup,1.0800576878867028,-54.73129768596024,0.24973618073585424,1,1
+optic_chiasm,0.284033040506682,1.0770896767813656,-11.15200025335908,1,1
+r_caud_head,15.32366873166477,17.418398352162686,10.282282403432571,1,1
+r_corp,28.065716932173196,-50.09742199619871,-35.8863924372445,1,1
+r_front_pole,9.282228865905484,53.64385773889343,20.359360383362517,1,1
+r_inner_corpus,0.3750664579883489,-18.621152492598828,20.04736016346814,1,1
+r_lat_ext,64.47685718089897,-31.456099309079985,-2.461208210665723,1,1
+r_occ_pole,18.026380089890477,-99.6971135427791,-7.188458824309168,1,1
+r_prim_ext,29.15692350632211,-37.323391086051096,-24.200298244358343,1,1
+r_sup_ext,7.062978169625272,-48.83078907071558,65.034736105428,1,1
+r_temp_pole,35.8308982781247,22.221251648850576,-20.059697985669054,1,1
+right_lateral_inner_ear,56.76557582293636,-10.852806094401668,-40.41078579756389,1,1
+rostrum,-0.10670269028927093,8.1435166054155,5.593083428764335,1,1
+rostrum_front,-0.16282452013595305,3.8353646742608043,17.37306179154106,1,1
+top_left,-21.019253567118948,27.911579557467853,47.07503850272812,1,1
+top_right,23.330261595397282,29.540558871893314,43.72661749307131,1,1

niftynet/contrib/fcsv_reader/fcsv_reader.py

@@ -0,0 +1,36 @@
+import numpy as np
+import pandas as pd
+from niftynet.layer.base_layer import Layer
+
+
+class FCSVReader(Layer):
+    def __init__(self, name="fcsv_reader"):
+        self.fid_pts = None
+        super(FCSVReader, self).__init__(name=name)
+
+    def initialise(self, path_to_fcsv, fiducials=["RE"]):
+        """
+         Assuming that the input file format is label,x,y,z,sel,vis
+        :param path_to_fcsv:
+        :param fiducials:
+        :return:
+        """
+        df = pd.read_csv(
+            path_to_fcsv,
+            header=None,
+            comment="#",
+            names=["fiducial_labels", "xcoord", "ycoord", "zcoord", "sel", "vis"],
+        )
+        self.fid_pts = {}
+        for fid in fiducials:
+            fid_df = df[df["fiducial_labels"] == fid]
+            # the sign flipping in x and y is to convert RAS(used by slicer) to LPS(used in DICOM and itk)
+            xcoord = -1 * fid_df["xcoord"].values.reshape(-1, 1)
+            ycoord = -1 * fid_df["ycoord"].values.reshape(-1, 1)
+            zcoord = fid_df["zcoord"].values.reshape(-1, 1)
+            one_d_vec = np.concatenate((xcoord, ycoord, zcoord), axis=1).reshape(-1, 1)
+            self.fid_pts[fid] = one_d_vec
+        return self
+
+    def layer_op(self, fid="RE"):
+        return self.fid_pts[fid]

niftynet/contrib/fcsv_reader/test_fcsv_reader.py

@@ -0,0 +1,8 @@
+from fcsv_reader import *
+
+my_fcsv_reader = FCSVReader()
+my_fcsv_reader = my_fcsv_reader.initialise(
+    path_to_fcsv="0001_27588.fcsv", fiducials=["LE", "RE"]
+)
+print(my_fcsv_reader.layer_op())
+print(my_fcsv_reader.layer_op(fid="LE"))