cleaning the repository

- more consistent module names
- removing a duplicate
- fixing new flake8 warnings

Vacations/convert.py

@@ -78,13 +78,13 @@ for f in os.listdir("."):
 
         has_weekday = False
 
-        for l in open(f, "r", encoding="utf8"):
-            if l.strip()[0] == "#":
-                if "Weekday" in l:
+        for line in open(f, "r", encoding="utf8"):
+            if line.strip()[0] == "#":
+                if "Weekday" in line:
                     has_weekday = True
                 continue
             # encoding issues with swedish:
-            lsp = l.split("  ")
+            lsp = line.split("  ")
             date = lsp[0].strip()
             if has_weekday:
                 i_desc = 2

Vacations/raw_convert.py

@@ -5,13 +5,13 @@ year = 2020
 
 fout = open(f"list_{year}.txt", "w")
 count = 0
-for l in open("orig.txt", "r"):
-    if len(l.strip()):
-        if "Date" in l:
+for line in open("orig.txt", "r"):
+    if len(line.strip()):
+        if "Date" in line:
             fout.write("# ")
-        fout.write(l[:-1])
+        fout.write(line[:-1])
         count += 1
-    elif len(l) == 1:
+    elif len(line) == 1:
         continue
     else:
         fout.write("  ")

ess/__init__.py

@@ -8,9 +8,9 @@ __all__ = [
     "fieldmap",
     "installed",
     "lib_tw",
-    "SP_Relativity",
+    "relativity",
     "TraceWin",
-    "TTF",
+    "ttf.py",
     "nextcloud",
 ]
 __version__ = "2.9.1"

ess/lib_tw.py

@@ -972,7 +972,7 @@ def plt2x(path_file):
             s.append(unpack("d", file.read(8))[0])
             phs.append(unpack("d", file.read(8))[0])
             ken.append(unpack("d", file.read(8))[0])
-            x.append([[unpack("f", file.read(4))[0] for l in range(7)] for k in range(Nptcl)])
+            x.append([[unpack("f", file.read(4))[0] for line in range(7)] for k in range(Nptcl)])
         except IndexError:
             break
 

ess/SP_Relativity.py → ess/relativity.py

@@ -182,7 +182,6 @@ def emit_norm(u_up_array, gamma):
     -------
     normalized emittance of the distribution/array in units of pi.mm.mrad
     """
-    # from ess import SP_Relativity as spr
     bt = beta_from_gamma(gamma)
     geo_emit = emit_geo(u_up_array)
     emit = bt * gamma * geo_emit

ess/TTF.py → ess/ttf.py

@@ -3,7 +3,7 @@ set of functions for calculating the transit time factor and the input phase res
 -- M. Eshraqi 2018 July 11
 """
 
-import SP_Relativity as myrel
+from . import relativity
 import numpy as np
 
 
@@ -57,7 +57,7 @@ def Field_TTF(field_1d, step_dz, freq, E_in, mass, RetMaxPhase):
                 dE += fval[0] * step_dz * np.cos(omega * t + d_phase * np.radians(phase))
                 if dE < 0:
                     print("Please adjust the field level, particle decelrated to zero energy!")
-                t += step_dz / (myrel.c * myrel.beta(dE, mass))
+                t += step_dz / (relativity.c * relativity.beta(dE, mass))
             if dE > Emax:
                 Emax = dE
                 phase_max = phase * d_phase
@@ -105,7 +105,7 @@ def TTF_beta(field_1d, step_dz, freq, mass):
     beta_out = 1
     TTFb[0, :] = np.arange(beta_in, beta_out, (beta_out - beta_in) / 50)
     for bt in TTFb[0, :]:
-        dummy = Field_TTF(field_1d, step_dz, freq, myrel.energy(bt, mass), mass, False)
+        dummy = Field_TTF(field_1d, step_dz, freq, relativity.energy(bt, mass), mass, False)
         TTFb[1, i] = dummy[0]
         i += 1
     return TTFb

examples/Binary_fieldmap/TTF.py

-"""
-set of functions for calculating the transit time factor and the input phase resulting in max energy gain in a field map
--- M. Eshraqi 2018 July 11
-"""
-
-import Batch_Convert_and_Cut_Binary_Fieldmap as bccb
-import SP_Relativity as myrel
-import numpy as np
-
-
-def field_on_axis(Field, fieldmap_dim, Nz, Nrx, Ny):
-    """
-    Take a 2D or 3D fieldmap as a 1D numpy array (as from TraceWin) in MV/m,
-    dimension of the fieldmap,
-    number of steps (No points - 1) in z direction,
-    number of steps in x/r direction, and
-    number of steps in the y direction (for 3D fieldmap) and
-    returns the field on-axis in the z direction
-    example:
-    field_on_axis(Field, 3, 100, 10, 10)
-    """
-    if fieldmap_dim == 2:
-        Fieldmapmatrix = np.reshape(Field, (int(Nz + 1), int(Nrx + 1)))
-        midpoint = int(Nrx / 2)
-    elif fieldmap_dim == 3:
-        Fieldmapmatrix = np.reshape(Field, (int(Nz + 1), int((Nrx + 1) * (Ny + 1))))
-        midpoint = int(Nrx * Ny / 2)
-    # print(midpoint)
-    return Fieldmapmatrix[:, midpoint]
-
-
-def Field_TTF(field_1d, step_dz, freq, E_in, mass, RetMaxPhase):
-    """
-    takes a 1D field on axis along the acceleration axis in MV/m,
-    the mesh size (length of each step),
-    frequency in MHz,
-    input energy in MeV,
-    mass in MeV and
-    RetMaxPhase as boolean
-    returns the TTF and at the given energy and
-    if RetMaxPhase==True returns also input phase resulting in max energy gain
-    """
-    omega = freq * 1e6 * 2 * np.pi
-    TTF_Phase = [0] * 2
-    dE = E_in
-    Emax = E_in
-    phase_max = 0
-    counter = 0
-    phase_start = 0
-    phase_end = 360
-    d_phase = 90
-
-    for iteration in np.arange(1, 10):
-        for phase in np.arange(int(phase_start / d_phase), int(phase_end / d_phase)):
-            counter += 1
-            t = 0
-            dE = E_in
-            for fval in field_1d:
-                dE += fval[0] * step_dz * np.cos(omega * t + d_phase * np.radians(phase))
-                # print(dE)
-                if dE < 0:
-                    print("Please adjust the field level, particle decelrated to zero energy!")
-                t += dz / (myrel.c() * myrel.beta(dE, mass))
-            if dE > Emax:
-                Emax = dE
-                # print('Emax', Emax)
-                phase_max = phase * d_phase
-        phase_start = phase_max - d_phase
-        phase_end = phase_max + d_phase
-        d_phase = d_phase / 4
-        if d_phase * 4 < 0.1:
-            break
-
-    # d_phase*=4
-    # print(counter, d_phase, phase_max, (Emax-E_in)/Field_integral(field_1d, dz))
-    TTF_Phase[0] = (Emax - E_in) / Field_integral(field_1d, dz)
-    if RetMaxPhase:
-        TTF_Phase[1] = phase_max
-    return TTF_Phase
-
-
-def Field_integral(field_1d, dz):
-    """
-    takes a 1D field on axis along the acceleration axis in MV/m,
-    the mesh size (length of each step) and
-    returns the rectangular integral of field
-    """
-    field_int = 0
-    for fval in field_1d:
-        # print(abs(fval[0]))
-        field_int += abs(fval[0])
-    return dz * field_int
-
-
-def TTF_beta(field_1d, step_dz, freq, mass):
-    """
-    takes a 1D field on axis along the acceleration axis in MV/m,
-    the mesh size (length of each step),
-    freq in MHz, and mass of particle in MeV and
-    returns a 2D array containig the TTF vs. beta. [Not very fast]
-    example
-    TTFarray = TTF_beta(one_d_field_on_axis, step_z, 704.42, 938)
-    beta_list = TTFarray[0]
-    TTF_list = TTFarray[1]
-    """
-    TTFb = np.zeros((2, 50))
-    i = 0
-    beta_in = 0.2
-    beta_out = 1
-    TTFb[0, :] = np.arange(beta_in, beta_out, (beta_out - beta_in) / 50)
-    for bt in TTFb[0, :]:
-        dummy = Field_TTF(field_1d, step_dz, freq, myrel.energy(bt, mass), mass, False)
-        TTFb[1, i] = dummy[0]
-        i += 1
-    return TTFb
-
-
-# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
-#                                                                                     #
-#                                    E X A M P L E S                                  #
-#                                                                                     #
-# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
-
-Header, Field = bccb.read_binary_fieldmap("Data/FM/HB_W_coupler.edz", 3)
-fz = field_on_axis(Field, 3, Header[0], Header[2], Header[5])
-z = np.arange(0, int(Header[0] + 1))
-dz = Header[1] / Header[0]
-z_points = dz * z
-
-print(
-    "Int_E:", Field_integral(fz, dz), "[TTF, Phase_Max_Energy]: ", Field_TTF(fz, dz, 704.42, 700, 938, True),
-)
-TTFb = TTF_beta(fz, dz, 704.42, 938)
-
-# plot(z_points, fz);
-# plot(TTFb[0,:], 50*TTFb[1,:]);

examples/manipulate_lattice/manipulate_lattice.py

@@ -55,7 +55,7 @@ err_comm_name = "MY_ERROR_COMMAND"
 err_comm_typ = "ERROR_CAV_NCPL_STAT"  # I know it's redundant but we also need this for now...
 err_comm_para = [0, 0, 0, 0, 0, 0, 0, 0, 0]  # This also works: err_comm_para=[0]*100
 
-err_comm = lib_tw.ERROR_CAV_NCPL_STAT(err_comm_name, err_comm_typ, err_comm_para)
+err_comm = lib_tw.lib_tw_elem.ERROR_CAV_NCPL_STAT(err_comm_name, err_comm_typ, err_comm_para)
 
 print("This is how it looks in the TraceWin syntax:")
 print(err_comm.get_tw(), "\n")

examples/ttf/ttf.py

-from ess import TTF
+from ess import ttf, fieldmap
 import numpy as np
 
-Header, Field = TTF.bccb.read_binary_fieldmap("Data/FM/HB_W_coupler.edz", 3)
-fz = TTF.field_on_axis(Field, 3, Header[0], Header[2], Header[5])
+Header, Field = fieldmap.read_fieldmap("Data/FM/HB_W_coupler.edz", 3, "b")
+fz = ttf.field_on_axis(Field, 3, Header[0], Header[2], Header[5])
 z = np.arange(0, int(Header[0] + 1))
 dz = Header[1] / Header[0]
 z_points = dz * z
 
 print(
-    "Int_E:", TTF.Field_integral(fz, dz), "[TTF, Phase_Max_Energy]: ", TTF.Field_TTF(fz, dz, 704.42, 700, 938, True),
+    "Int_E:", ttf.Field_integral(fz, dz), "[TTF, Phase_Max_Energy]: ", ttf.Field_TTF(fz, dz, 704.42, 700, 938, True),
 )
-TTFb = TTF.TTF_beta(fz, dz, 704.42, 938)
+TTFb = ttf.TTF_beta(fz, dz, 704.42, 938)
 
 # plot(z_points, fz);
 # plot(TTFb[0,:], 50*TTFb[1,:]);

scripts/tracewin

@@ -39,7 +39,7 @@ args = parser.parse_args()
 
 # A list to be filled depending on arguments given...
 binary = None
-for c in ["TraceWin64_noX11", "TraceWin_cli"]:
+for c in ["TraceWin_noX11", "TraceWin_cli"]:
     if shutil.which(c):
         binary = c
         break

scripts/tracewin_errorstudy

@@ -167,9 +167,9 @@ def setup_multi(args):
 
     # Get random seeds from previously run jobs:
     seeds = []
-    for l in open(os.path.join(args.calc_dir, "submit.job"), "r"):
-        if len(l.strip()) and l.split()[0] == "arguments":
-            seeds.append(l.split()[-1])
+    for line in open(os.path.join(args.calc_dir, "submit.job"), "r"):
+        if len(line.strip()) and line.split()[0] == "arguments":
+            seeds.append(line.split()[-1])
 
     head_template = __queue_templates__.get_head_multi_template()
     queue_template = __queue_templates__.get_queue_multi_template()