libamtrack / library Goto Github PK

(pyamtrack1) grzanka@grzanka-VirtualBox:~$ pip install pyamtrack
Collecting pyamtrack
  Downloading https://files.pythonhosted.org/packages/27/ad/2c0e74c8b53fe8aa1e2c87b4002fb6b816bf83541c384c9c45551c7cdf3a/pyamtrack-0.1.1-py3-none-manylinux1_x86_64.whl (4.8MB)
     |████████████████████████████████| 4.8MB 1.1MB/s 
Collecting cffi>=1.13.0
  Downloading https://files.pythonhosted.org/packages/16/cd/1f4ddf6be8300713c676bb9f3a2d3b8eb8accc0a6a24f57d4f6c4cd59d34/cffi-1.13.2-cp37-cp37m-manylinux1_x86_64.whl (398kB)
     |████████████████████████████████| 399kB 53.8MB/s 
Processing ./.cache/pip/wheels/f2/9a/90/de94f8556265ddc9d9c8b271b0f63e57b26fb1d67a45564511/pycparser-2.19-py2.py3-none-any.whl
Installing collected packages: pycparser, cffi, pyamtrack
Successfully installed cffi-1.13.2 pyamtrack-0.1.1 pycparser-2.19
(pyamtrack1) grzanka@grzanka-VirtualBox:~$ python
Python 3.7.6 (default, Jan  8 2020, 19:59:22) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pyamtrack import libAT
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/grzanka/.conda/envs/pyamtrack1/lib/python3.7/site-packages/pyamtrack/libAT.py", line 2, in <module>
    from .lib import _libAT
ImportError: cannot import name '_libAT' from 'pyamtrack.lib' (/home/grzanka/.conda/envs/pyamtrack1/lib/python3.7/site-packages/pyamtrack/lib/__init__.py)
>>> 
(pyamtrack1) grzanka@grzanka-VirtualBox:~$ python -V
Python 3.7.6

/**
 * Computes the convolution of a term (R0 - z)^(ni - 1) with a Gaussian
 * in z with variance sigma^2, i.e.
 * F(z, R0) = 1/(2*pi*sigma) * int_{-inf}^{R0}[ (R0 - z)^(ni - 1) * exp(-(z - z')^2/(2*sigma^2)) * dz']
 * that can be solved using the gamma function and the parabolic cylinder function:
 * F(z, R0) = 1/(2*pi*sigma) * exp((R0 - z)/(4*sigma^2)) * sigma^ni * gamma(ni) * D[-ni](-(R0-z)/sigma)
 * where D[-ni] is the parabolic cylinder function of order -ni
 *
 * The procedure is elucidated in Bortfeld, 1997, An analytical approximation of the Bragg curve for therapeutic
 * proton beams, Med. Phys. 24(12), 2024ff., Appendix A, Eqs. A1, A6
 *
 * This function uses gamma_ and AT_Dyx.
 *
 * Cave: Be careful to give the correct ni (not ni - 1)!
 *
 * @param[in]   z
 * @param[in]   R0
 * @param[in]   sigma
 * @param[in]   ni
 * @return      funs
 */
double AT_range_straggling_convolution(  const double z,
    const double R0,
    const double sigma,
    const double ni);

> install.packages('libamtrack', repos='http://R-Forge.R-project.org')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/Legion/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Package which is only available in source form, and may need
  compilation of C/C++/Fortran: ‘libamtrack’
  These will not be installed

  const double b1_g_cm2 = 0.2335;
  const double b2 = 1.209;
  const double b3 = 1.78e-4;
  const double b4 = 0.9891;
  const double b5 = 3.01e-4;
  const double b6 = 1.468;
  const double b7 = 1.18e-2;
  const double b8 = 1.232;
  const double b9 = 0.109;
  // constants...
  *a1_g_cm2 = b1_g_cm2*average_A / pow(average_Z,b2);
  *a2 = b3*average_A;
  *a3 = b4 - b5*average_Z;
  *a4 = b6 - b7*average_Z;
  *a5 = b8 / pow(average_Z,b9);

/io/library/src/AT_SuccessiveConvolutions.c: In function ‘AT_single_impact_local_dose_distrib’:
/io/library/src/AT_SuccessiveConvolutions.c:330:11: error: conflicting types for ‘j’
  for (int j = 0; j < n_bins_f1; j++){
           ^
/io/library/src/AT_SuccessiveConvolutions.c:120:10: note: previous declaration of ‘j’ was here
  long i, j;
          ^
/io/library/src/AT_SuccessiveConvolutions.c:330:2: error: ‘for’ loop initial declarations are only allowed in C99 mode
  for (int j = 0; j < n_bins_f1; j++){
  ^
/io/library/src/AT_SuccessiveConvolutions.c:330:2: note: use option -std=c99 or -std=gnu99 to compile your code
/io/library/src/AT_SuccessiveConvolutions.c: In function ‘AT_n_bins_for_DSB_distribution’:
/io/library/src/AT_SuccessiveConvolutions.c:1043:4: error: ‘for’ loop initial declarations are only allowed in C99 mode
    for(long i = 0; i < n_bins_f; i++){
    ^
/io/library/src/AT_SuccessiveConvolutions.c: In function ‘AT_get_DSB_distribution’:
/io/library/src/AT_SuccessiveConvolutions.c:1079:4: error: ‘for’ loop initial declarations are only allowed in C99 mode
    for(long i = 0; i < n_bins_f; i++){
    ^
/io/library/src/AT_SuccessiveConvolutions.c:1091:13: error: redefinition of ‘i’
    for(long i = 0; i < max_number_of_DSBs; i++){
             ^
/io/library/src/AT_SuccessiveConvolutions.c:1079:13: note: previous definition of ‘i’ was here
    for(long i = 0; i < n_bins_f; i++){
             ^
/io/library/src/AT_SuccessiveConvolutions.c:1091:4: error: ‘for’ loop initial declarations are only allowed in C99 mode
    for(long i = 0; i < max_number_of_DSBs; i++){
    ^
/io/library/src/AT_SuccessiveConvolutions.c:1094:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for(long j = 0; j < n_bins_f; j++){
     ^
/io/library/src/AT_SuccessiveConvolutions.c:1096:16: error: ‘NAN’ undeclared (first use in this function)
     p_DSB[i] = NAN;
                ^
/io/library/src/AT_SuccessiveConvolutions.c:1096:16: note: each undeclared identifier is reported only once for each function it appears in
/io/library/src/AT_SuccessiveConvolutions.c: In function ‘AT_translate_dose_into_DSB_distribution’:
/io/library/src/AT_SuccessiveConvolutions.c:1173:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for(long i = 0; i < n_bins_DSB; i++){
     ^

funs+='"_AT_lambda_max_multi",' 
funs+='"_AT_lambda_max_single",' 
funs+='"_AT_lambda_Landau_Mode()",' 
funs+='"_AT_lambda_Landau_Mean(cons",' 
funs+='"_AT_lambda_Landau_FWHM_left()",' 
funs+='"_AT_lambda_Landau_FWHM_right()",' 
funs+='"_AT_lambda_Landau_FWHM()",' 
funs+='"_AT_energy_loss_keV_Landau_FWHM(cons",' 
funs+='"_AT_energy_loss_keV_Landau_Mode(cons",' 
funs+='"_AT_energy_loss_from_lambda_landau_multi",' 
funs+='"_AT_energy_loss_from_lambda_landau_single",' 
funs+='"_AT_Landau_energy_loss_distribution",' 

python version: Python 3.6.9
pip version: pip 20.0.1 from /usr/local/lib/python3.6/dist-packages/pip (python 3.6)

pip install pyamtrack

ERROR: Could not find a version that satisfies the requirement pyamtrack (from versions: none)
ERROR: No matching distribution found for pyamtrack

void AT_dose_Bortfeld_Gy_multi(const long n,
                               const double z_cm[],
                               const double fluence_cm2,
                               const double E_MeV_u,
                               const double sigma_E_MeV_u,
                               const long material_no,
                               const double eps,
                               double dose_Gy[]) {
    long i;
    for (i = 0; i < n; i++) {
        dose_Gy[i] = AT_dose_Bortfeld_Gy_single(z_cm[i], E_MeV_u, fluence_cm2, sigma_E_MeV_u, material_no, eps);
    }
}```