Read write FBR format

bvbabel/__init__.py

@@ -21,3 +21,4 @@
 import bvbabel.roi
 import bvbabel.glm
 import bvbabel.dmr
+import bvbabel.fbr

bvbabel/fbr.py

@@ -0,0 +1,175 @@
+""" Read BrainVoyager FBR file format."""
+
+import numpy as np
+import re
+
+# =============================================================================
+def read_fbr(filename):    
+    """Read Brainvoyager FBR file
+
+    https://helpdesk.brainvoyager.com/603922-The-Format-of-FBR-Files
+
+    Parameters
+    ----------
+    filename : string
+        Path to file.
+
+    Returns
+    -------
+    header : dictionary
+        Fiber (FBR) header. 
+    data : 
+        Fiber points
+
+
+    Description FBR file format
+
+    Parameter       Sample value     Description 	
+    -------------   ---------        -----------
+
+    FileVersion:	4               File version of the *.fbr file
+
+    CoordsType:     BV I            BrainVoyager coordinate system
+
+    FibersOriginX:  128             Origin of fibers (FileVersion 4)
+    FibersOriginY:  128
+    FibersOriginZ:  128
+
+    NrOfGroups:	    1
+
+    Name:	        "Tracked From VOI: testvoi_ACPC"
+
+    Visible:	    1               Boolean value indicating whether the fiber should be shown
+    Animate:	    -1
+
+    Thickness:	    0.3             Thickness of the shown fiber in mm (?)
+    Color:	        25 25 127       RGB values for fiber (between 0 and 255)
+    NrOfFibers:	    121
+
+    [Loop over number of fibers:]	
+
+        NrOfPoints:	    <int>
+        (3x float 3x int)	101.209 128.266 120.192     156 148 135
+
+        For example: 
+
+        NrOfPoints:    2
+        101.209 128.266 120.192    156 148 135
+        101.5 128 120.5    156 148 135
+
+
+    Newer information (see DTI Getting Started Guide 1.1):
+
+        This is the coordinate system in the OpenGL/3D Viewer window.
+        Origin: [x, y, z] = 0.5*VMR slice X-resolution, 0.5*VMR slice Y-resolution, 0.5*number of slices 
+        x-axis: anterior to posterior 0 to X-resolution 
+        y-axis: superior to inferior 0 to Y-resolution 
+        z-axis: right to left 0 to Z-resolution
+
+    """
+
+    # Read non-empty lines of the input text file
+    with open(filename, 'r') as f:
+        lines = [r for r in (line.strip() for line in f) if r]
+
+    # FBR header
+    header = dict()
+    n_header_rows = 12 # = no of rows without empty lines
+    for line in lines[0:(n_header_rows)]:#-2)]:
+        content = line.split(":")
+        content = [i.strip() for i in content]
+        if content[1].isdigit():
+            header[content[0]] = int(content[1])
+        else:
+            header[content[0]] = content[1]
+
+    colors = lines[10].split(" ")
+    colors = [c.strip(" ") for c in colors]
+    colors2 = []
+    for c in range(len(colors)):
+        if colors[c].isdigit():
+            colors2.append(int(colors[c]))               
+    header["Color"] = colors2
+
+    count_fbr = -1
+    data_fbr = list()
+    p = re.compile(r'\d+(\.\d+)?$') # regular expression for detecting floats, isdigits() does not work
+    for line in lines[n_header_rows:]: # loop from end of header to end of file
+
+        if "NrOfPoints" in line:   
+            content = line.split(":")
+            content = [i.strip() for i in content]
+            count_fbr += 1
+            data_fbr.append(dict())
+            data_fbr[count_fbr]["NrOfPoints"] = int(content[1])
+            data_fbr[count_fbr]["Points"] = []  # prepare for coordinates
+        else: # points content
+            values = line.split(" ")
+            points = []
+            for v in values:
+                if v.isdigit():
+                    points.append(int(v.strip()) ) 
+                elif p.match(v):    
+                    points.append(float(v.strip()) ) 
+            data_fbr[count_fbr]["Points"].append(points)
+
+    return header, data_fbr            
+
+
+
+def write_fbr(filename, header, data_fbr):
+    """Function to write BrainVoyager FBR file.
+
+    Parameters
+    ----------
+    filename : string
+        Path to file.
+    header : dictionary
+        Fibers (FBR) header.
+    data_fbr : list of dictionaries
+        A list of dictionaries. Each dictionary holds coordinates of a fiber.
+
+    """
+
+    with open(filename, 'w') as f:
+
+        data = header["FileVersion"]
+        f.write("FileVersion:\t{}\n".format(data))
+        data = header["CoordsType"]
+        f.write("CoordsType:\t{}\n".format(data))
+        data = header["FibersOriginX"]
+        f.write("FibersOriginX:\t{}\n".format(data))
+        data = header["FibersOriginY"]
+        f.write("FibersOriginY:\t{}\n".format(data))
+        data = header["FibersOriginZ"]
+        f.write("FibersOriginZ:\t{}\n".format(data))      
+        f.write("\n")
+        data = header["NrOfGroups"]
+        f.write("NrOfGroups:\t{}\n".format(data))        
+        f.write("\n")
+        data = header["Name"]
+        f.write("Name:\t\t{}\n".format(data))   
+        data = header["Visible"]
+        f.write("Visible:\t{}\n".format(data))           
+        data = header["Animate"]
+        f.write("Animate:\t{}\n".format(data))   
+        data = header["Thickness"]
+        f.write("Thickness:\t{}\n".format(data))   
+        data = header["Color"]
+        f.write("Color:\t\t{} {} {}\n".format(data[0], data[1], data[2]))
+        f.write("\n")
+        data = header["NrOfFibers"]
+        f.write("NrOfFibers:\t{}\n".format(data))     
+        f.write("\n")
+
+        # ---------------------------------------------------------------------
+        # FBR data
+
+        for p in data_fbr:
+            data = p["NrOfPoints"]
+            f.write("NrOfPoints:\t{}\n".format(data))
+            data = p["Points"]
+            for d in data:
+                f.write("{:.3f} {:.3f} {:.3f}    {:n} {:n} {:n}\n".format(d[0], d[1], d[2], d[3], d[4], d[5]))
+            f.write("\n")
+

examples/read_write_fbr.py

@@ -0,0 +1,21 @@
+"""Read and write BrainVoyager FBR (diffusion weighted data: fiber reconstruction) file."""
+
+import os
+import bvbabel
+from pprint import pprint
+
+FILE = "/Users/hester_1/Progprojs/Python/2024/fbr/testvoi_DWI_b3000_PA_ACPC_132dirs_11x0_masked.fbr"
+
+# =============================================================================
+# Load FBR
+header, data = bvbabel.fbr.read_fbr(FILE)
+
+# See header information
+pprint(header)
+
+# Save FBR
+basename = FILE.split(os.extsep, 1)[0]
+outname = "{}_bvbabel.fbr".format(basename)
+bvbabel.fbr.write_fbr(outname, header, data)
+
+print("Finished.")