Merge pull request #96 from compSPI/luis_master

Luis master

.github/workflows/build_container.yml

@@ -2,7 +2,7 @@ name: "Building simSPI Container"
 
 on:
   push:
-    branches: [master, github-actions-test, refactoring]
+    branches: [master, github-actions-test, update-container]
     paths:
       - 'docker/Dockerfile'
       - 'docker/entrypoint.sh'

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
           - --maxkb=2048
       - id: trailing-whitespace
   - repo: https://github.com/psf/black
-    rev: 22.1.0
+    rev: 22.3.0
     hooks:
       - id: black
   - repo: https://github.com/pycqa/isort

docker/.dockerignore

@@ -0,0 +1,11 @@
+.github
+.pytest_cache
+data
+simSPI.egg-info
+.deepsource.toml
+.gitignore
+.pre-commit-config.yaml
+dev-requirements.txt
+environment-mac.yml
+path-config.yaml
+sim-config.yaml

docker/Dockerfile

@@ -30,17 +30,18 @@ RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh &
     rm /work/Miniconda3-latest-Linux-x86_64.sh
 
 # Copy the code and generate the environment
+COPY . /work/
 # Remains to be done: COPY all and remove the fat later, instead-of multiplying layers:
-COPY environment.yml /work/environment.yml
-COPY README.md /work/README.md
-COPY setup.py /work/setup.py
-COPY pytest.ini /work/pytest.ini
-COPY .codecov.yml /work/.codecov.yml
-COPY .coveragerc /work/.coveragerc
-COPY .flake8 /work/.flake8
-COPY simSPI /work/simSPI
-COPY notebooks /work/notebooks
-COPY tests /work/tests
+#COPY environment.yml /work/environment.yml
+#COPY README.md /work/README.md
+#COPY setup.py /work/setup.py
+#COPY pytest.ini /work/pytest.ini
+#COPY .codecov.yml /work/.codecov.yml
+#COPY .coveragerc /work/.coveragerc
+#COPY .flake8 /work/.flake8
+#COPY simSPI /work/simSPI
+#COPY notebooks /work/notebooks
+#COPY tests /work/tests
 RUN . /opt/anaconda/etc/profile.d/conda.sh && conda update -c conda-forge conda
 RUN . /opt/anaconda/etc/profile.d/conda.sh && \
     conda env update --name base --file environment.yml && \

environment-mac.yml

@@ -20,6 +20,8 @@ dependencies:
     - geomstats
     - git+https://github.com/compSPI/compSPI.git
     - git+https://github.com/compSPI/ioSPI.git
+    - jupyterlab
+    - papermill
     - pytorch3d
     - raster_geometry
     - starfile

notebooks/metadata_fields.yaml

@@ -0,0 +1,33 @@
+  seed: "seed"
+  log_file: "log_file"
+  signal_to_noise: "signal_to_noise"
+  diameter: "hole_diameter_nm"
+  thickness_center: "hole_thickness_center_nm"
+  thickness_edge: "hole_thickness_edge_nm"
+  name: "particle_name"
+  voxel_size: "voxel_size_nm"
+  pdb_file: "pdb_file"
+  map_file_re_out: "map_file_re_out"
+  map_file_im_out: "map_file_im_out"
+  crd_file: "crd_file"
+  voltage: "voltage_kv"
+  spread: "energy_spread_v"
+  dose_per_im: "electron_dose_e_per_nm2"
+  dose_sd: "electron_dose_std_e_per_nm2"
+  magnification: "magnification"
+  cs: "spherical_aberration_mm"
+  cc: "chromatic_aberration_mm"
+  aperture: "aperture_diameter_um"
+  focal_length: "focal_length_mm"
+  cond_ap_angle: "aperture_angle_mrad"
+  defocus_nominal: "defocus_um"
+  defocus_syst_error: "defocus_syst_error_um"
+  defocus_nonsyst_error: "defocus_nonsyst_error_um"
+  defocus_file_out: "optics_defocusout"
+  det_pix_x: "detector_nx_px"
+  det_pix_y: "detector_ny_px"
+  pixel_size: "detector_pixel_size_um"
+  gain: "average_gain_count_per_electron"
+  use_quantization: "noise"
+  dqe: "detector_q_efficiency"
+  image_file_out: "image_file_out"

notebooks/path_config.yaml

@@ -0,0 +1,7 @@
+#
+  pdb_file: './notebooks/4v6x.pdb'
+  metadata_params_file: './notebooks/metadata_fields.yaml'
+  mrc_keyword: '_randomrot'
+  output_dir: './notebooks/'
+  local_sim_dir: '/work/TEM-simulator_1.3/src/TEM-simulator'
+

notebooks/sim_config.yaml

@@ -0,0 +1,48 @@
+  # References:
+  # TEM-simulator version 1.3 user manual
+  # http://tem-simulator.sourceforge.net/
+
+  molecular_model:
+    voxel_size_nm: 0.1         # the size of voxels in the particle map in nm. Range : [0.1,100].
+    particle_name: 'toto'      # name of the particle.
+    particle_mrcout: None      # volume map of sample is written.
+
+  specimen_grid_params:
+    hole_diameter_nm: 1200         # the diameter of the sample in nm.
+    hole_thickness_center_nm: 100  # the thickness of the sample at the center in nm.
+    hole_thickness_edge_nm: 100    # The thickness of the sample at the edge and the surrounding support in nm.
+    particle_slice_pad: 5          # padding around each projected particle in px.
+
+  beam_parameters:
+    voltage_kv: 300                  # the acceleration voltage of the microscope in kV. Range : [1,10^4].
+    energy_spread_v: 1.3             # the energy spread of the electron beam in V.
+    electron_dose_e_per_nm2: 100     # dose per image in e/nm**2
+    electron_dose_std_e_per_nm2: 0   # standard deviation of dose per image. Range : [0,1]. Default : 0.
+
+  optics_parameters:
+    magnification: 81000        # the magnification of the simulated microscope. Range : > 1.
+    spherical_aberration_mm: 0.0    # the spherical aberration of the optical system in mm.
+    chromatic_aberration_mm: 0.0     # the chromatic aberration of the optical system in mm.
+    aperture_diameter_um: 50         # diameter of aperture in back focal plane in μm.
+    focal_length_mm: 3.5             # the focal length of primary lens in mm.
+    aperture_angle_mrad: 0.1         # the aperture angle of beam furnished by condenser lens in mrad.
+    defocus_um: 0.0                  # [μm]
+    defocus_syst_error_um: 0.0       # [μm]
+    defocus_nonsyst_error_um: 0.0    # [μm]
+    optics_defocusout: None     # file to write defocus values
+
+  detector_parameters:
+    detector_nx_px: 5760               # number of pixels along X axis.Range : [1,10^4].
+    detector_ny_px: 4092               # number of pixels along Y axis.Range : [1,10^4].
+    detector_pixel_size_um: 5          # The physical size of the detector pixels in μm. Range : [10^-2,10^3].
+    average_gain_count_per_electron: 2 # average number of counts produced per electron.
+    noise: 'no'                 # quantise electron wave as discrete electrons (produces detector noise). Range : [yes,no].
+    detector_q_efficiency: 0.5  # detector quantum efficiency. Range : [10^-2,1]. Only used if noise is 'yes'.
+    mtf_params: [0,0,1,0,0]     # parameters [mtf_a,mtf_b,mtf_c,mtf_alpha,mtf_beta] specifying the shape of the Modular
+                                # Transfer Function. [0,0,1,0,0] is perfect detector.
+
+  geometry_parameters:
+    n_samples: 1                       # number of samples to be generated.
+
+  miscellaneous:
+   seed : 1234                 # seed for simulator.