remove fsl deps, containerization wip

Dockerfile

@@ -0,0 +1,9 @@
+FROM python:3.8-slim
+
+COPY . /gradunwarp
+
+RUN cd /gradunwarp \
+  && pip install -r requirements.txt \
+  && pip install .
+
+ENTRYPOINT ["/usr/local/bin/gradient_unwarp.py"]

gradunwarp/core/coeffs.py

@@ -13,119 +13,131 @@
 from .globals import siemens_cas, ge_cas
 
 
-log = logging.getLogger('gradunwarp')
+log = logging.getLogger("gradunwarp")
 
 
-Coeffs = namedtuple('Coeffs', 'alpha_x, alpha_y, alpha_z, \
-                        beta_x, beta_y, beta_z, R0_m')
+Coeffs = namedtuple(
+    "Coeffs",
+    "alpha_x, alpha_y, alpha_z, \
+                        beta_x, beta_y, beta_z, R0_m",
+)
 
 try:
     advance_iterator = next
 except NameError:
+
     def advance_iterator(it):
         return it.next()
+
+
 next = advance_iterator
 
 
 def get_coefficients(vendor, cfile):
-    ''' depending on the vendor and the coefficient file,
+    """depending on the vendor and the coefficient file,
     return the spherical harmonics coefficients as a named tuple.
-    '''
-    log.info('Parsing ' + cfile + ' for harmonics coeffs')
-    if vendor == 'siemens' and cfile.endswith('.coef'):
+    """
+    log.info("Parsing " + cfile + " for harmonics coeffs")
+    if vendor == "siemens" and cfile.endswith(".coef"):
         return get_siemens_coef(cfile)
-    if vendor == 'siemens' and cfile.endswith('.grad'):
+    if vendor == "siemens" and cfile.endswith(".grad"):
         return get_siemens_grad(cfile)
 
 
 def coef_file_parse(cfile, txt_var_map):
-    ''' a separate function because GE and Siemens .coef files
+    """a separate function because GE and Siemens .coef files
     have similar structure
 
     modifies txt_var_map in place
-    '''
+    """
     # parse .coef file. Strip unneeded characters. a valid line in that file is
     # broken into validline_list
-    coef_re = re.compile('^[^\#]')  # regex for first character not a '#'
-    coef_file = open(cfile, 'r')
+    coef_re = re.compile("^[^\#]")  # regex for first character not a '#'
+    coef_file = open(cfile, "r")
     for line in coef_file.readlines():
         if coef_re.match(line):
-            validline_list = line.lstrip(' \t').rstrip(';\n').split()
+            validline_list = line.lstrip(" \t").rstrip(";\n").split()
             if validline_list:
-                log.info('Parsed : %s' % validline_list)
+                log.info("Parsed : %s" % validline_list)
                 l = validline_list
                 x = int(l[1])
                 y = int(l[2])
                 txt_var_map[l[0]][x, y] = float(l[3])
 
 
 def get_siemens_coef(cfile):
-    ''' Parse the Siemens .coef file.
+    """Parse the Siemens .coef file.
     Note that R0_m is not explicitly contained in the file
-    '''
-    R0m_map = {'sonata': 0.25,
-               'avanto': 0.25,
-               'quantum': 0.25,
-               'allegra': 0.14,
-               'as39s': 0.25,
-               'as39st': 0.25,
-               'as39t': 0.25}
+    """
+    R0m_map = {
+        "sonata": 0.25,
+        "avanto": 0.25,
+        "quantum": 0.25,
+        "allegra": 0.14,
+        "as39s": 0.25,
+        "as39st": 0.25,
+        "as39t": 0.25,
+    }
     for rad in R0m_map.keys():
         if cfile.startswith(rad):
             R0_m = R0m_map[rad]
 
     coef_array_sz = siemens_cas
     # allegra is slightly different
-    if cfile.startswith('allegra'):
+    if cfile.startswith("allegra"):
         coef_array_sz = 15
     ax = np.zeros((coef_array_sz, coef_array_sz))
     ay = np.zeros((coef_array_sz, coef_array_sz))
     az = np.zeros((coef_array_sz, coef_array_sz))
     bx = np.zeros((coef_array_sz, coef_array_sz))
     by = np.zeros((coef_array_sz, coef_array_sz))
     bz = np.zeros((coef_array_sz, coef_array_sz))
-    txt_var_map = {'Alpha_x': ax,
-                   'Alpha_y': ay,
-                   'Alpha_z': az,
-                   'Beta_x': bx,
-                   'Beta_y': by,
-                   'Beta_z': bz}
+    txt_var_map = {
+        "Alpha_x": ax,
+        "Alpha_y": ay,
+        "Alpha_z": az,
+        "Beta_x": bx,
+        "Beta_y": by,
+        "Beta_z": bz,
+    }
 
     coef_file_parse(cfile, txt_var_map)
 
     return Coeffs(ax, ay, az, bx, by, bz, R0_m)
 
 
 def get_ge_coef(cfile):
-    ''' Parse the GE .coef file.
-    '''
+    """Parse the GE .coef file."""
     ax = np.zeros((ge_cas, ge_cas))
     ay = np.zeros((ge_cas, ge_cas))
     az = np.zeros((ge_cas, ge_cas))
     bx = np.zeros((ge_cas, ge_cas))
     by = np.zeros((ge_cas, ge_cas))
     bz = np.zeros((ge_cas, ge_cas))
-    txt_var_map = {'Alpha_x': ax,
-                   'Alpha_y': ay,
-                   'Alpha_z': az,
-                   'Beta_x': bx,
-                   'Beta_y': by,
-                   'Beta_z': bz}
+    txt_var_map = {
+        "Alpha_x": ax,
+        "Alpha_y": ay,
+        "Alpha_z": az,
+        "Beta_x": bx,
+        "Beta_y": by,
+        "Beta_z": bz,
+    }
 
     coef_file_parse(cfile, txt_var_map)
 
     return Coeffs(ax, ay, az, bx, by, bz, R0_m)
 
+
 def grad_file_parse(gfile, txt_var_map):
-    ''' a separate function because GE and Siemens .coef files
+    """a separate function because GE and Siemens .coef files
     have similar structure
 
     modifies txt_var_map in place
-    '''
-    gf = open(gfile, 'r')
+    """
+    gf = open(gfile, "r")
     line = next(gf)
     # skip the comments
-    while not line.startswith('#*] END:'):
+    while not line.startswith("#*] END:"):
         line = next(gf)
 
     # get R0
@@ -147,30 +159,30 @@ def grad_file_parse(gfile, txt_var_map):
     ymax = 0
 
     while 1:
-        lindex =  line.find('(')
-        rindex =  line.find(')')
+        lindex = line.find("(")
+        rindex = line.find(")")
         if lindex == -1 and rindex == -1:
             break
-        arrindex = line[lindex+1:rindex]
-        xs, ys = arrindex.split(',')
-        x = int(xs) 
+        arrindex = line[lindex + 1 : rindex]
+        xs, ys = arrindex.split(",")
+        x = int(xs)
         y = int(ys)
         if x > xmax:
             xmax = x
         if y > ymax:
             ymax = y
-        if line.find('A') != -1 and line.find('x') != -1:
-            txt_var_map['Alpha_x'][x,y] = float(line.split()[-2])
-        if line.find('A') != -1 and line.find('y') != -1:
-            txt_var_map['Alpha_y'][x,y] = float(line.split()[-2])
-        if line.find('A') != -1 and line.find('z') != -1:
-            txt_var_map['Alpha_z'][x,y] = float(line.split()[-2])
-        if line.find('B') != -1 and line.find('x') != -1:
-            txt_var_map['Beta_x'][x,y] = float(line.split()[-2])
-        if line.find('B') != -1 and line.find('y') != -1:
-            txt_var_map['Beta_y'][x,y] = float(line.split()[-2])
-        if line.find('B') != -1 and line.find('z') != -1:
-            txt_var_map['Beta_z'][x,y] = float(line.split()[-2])
+        if line.find("A") != -1 and line.find("x") != -1:
+            txt_var_map["Alpha_x"][x, y] = float(line.split()[-2])
+        if line.find("A") != -1 and line.find("y") != -1:
+            txt_var_map["Alpha_y"][x, y] = float(line.split()[-2])
+        if line.find("A") != -1 and line.find("z") != -1:
+            txt_var_map["Alpha_z"][x, y] = float(line.split()[-2])
+        if line.find("B") != -1 and line.find("x") != -1:
+            txt_var_map["Beta_x"][x, y] = float(line.split()[-2])
+        if line.find("B") != -1 and line.find("y") != -1:
+            txt_var_map["Beta_y"][x, y] = float(line.split()[-2])
+        if line.find("B") != -1 and line.find("z") != -1:
+            txt_var_map["Beta_z"][x, y] = float(line.split()[-2])
         try:
             line = next(gf)
         except StopIteration:
@@ -179,36 +191,37 @@ def grad_file_parse(gfile, txt_var_map):
     # just return R0_m but also txt_var_map is returned
     return R0_m, (xmax, ymax)
 
+
 def get_siemens_grad(gfile):
-    ''' Parse the siemens .grad file
-    '''
+    """Parse the siemens .grad file"""
     coef_array_sz = siemens_cas
     # allegra is slightly different
-    if gfile.startswith('coef_AC44'):
+    if gfile.startswith("coef_AC44"):
         coef_array_sz = 15
     ax = np.zeros((coef_array_sz, coef_array_sz))
     ay = np.zeros((coef_array_sz, coef_array_sz))
     az = np.zeros((coef_array_sz, coef_array_sz))
     bx = np.zeros((coef_array_sz, coef_array_sz))
     by = np.zeros((coef_array_sz, coef_array_sz))
     bz = np.zeros((coef_array_sz, coef_array_sz))
-    txt_var_map = {'Alpha_x': ax,
-                   'Alpha_y': ay,
-                   'Alpha_z': az,
-                   'Beta_x': bx,
-                   'Beta_y': by,
-                   'Beta_z': bz}
+    txt_var_map = {
+        "Alpha_x": ax,
+        "Alpha_y": ay,
+        "Alpha_z": az,
+        "Beta_x": bx,
+        "Beta_y": by,
+        "Beta_z": bz,
+    }
 
     R0_m, max_ind = grad_file_parse(gfile, txt_var_map)
     ind = max(max_ind)
 
     # pruned alphas and betas
-    ax = ax[:ind+1, :ind+1]
-    ay = ay[:ind+1, :ind+1]
-    az = az[:ind+1, :ind+1]
-    bx = bx[:ind+1, :ind+1]
-    by = by[:ind+1, :ind+1]
-    bz = bz[:ind+1, :ind+1]
+    ax = ax[: ind + 1, : ind + 1]
+    ay = ay[: ind + 1, : ind + 1]
+    az = az[: ind + 1, : ind + 1]
+    bx = bx[: ind + 1, : ind + 1]
+    by = by[: ind + 1, : ind + 1]
+    bz = bz[: ind + 1, : ind + 1]
 
     return Coeffs(ax, ay, az, bx, by, bz, R0_m)
-

gradunwarp/core/globals.py

@@ -6,20 +6,20 @@
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 import logging
 
-VERSION = '1.2.1+HCP'
+VERSION = "1.2.1+HCP"
 
-usage = '''
+usage = """
 gradient_unwarp infile outfile manufacturer -g <coefficient file> [optional arguments]
-'''
+"""
 
 
 # SIEMENS stuff
 siemens_cas = 100  # coefficient array size
-siemens_fovmin = -.30  # fov min in meters
-siemens_fovmax = .30  # fov max in meters
-siemens_numpoints = 60 # number of grid points in each direction
+siemens_fovmin = -0.30  # fov min in meters
+siemens_fovmax = 0.30  # fov max in meters
+siemens_numpoints = 60  # number of grid points in each direction
 # max jacobian determinant for siemens
-siemens_max_det = 10.
+siemens_max_det = 10.0
 
 
 # GE stuff
@@ -30,7 +30,7 @@
 
 
 def get_logger():
-    log = logging.getLogger('gradunwarp')
+    log = logging.getLogger("gradunwarp")
     log.setLevel(logging.INFO)
     ch = logging.StreamHandler()
     ch.setLevel(logging.INFO)