From 18d9f5aa8b3846437231cc1e36db38c316fc8c79 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Mon, 20 Jan 2025 15:22:36 -0500
Subject: [PATCH 01/22] added submodule

---
 .gitmodules | 3 +++
 plastimatch | 1 +
 2 files changed, 4 insertions(+)
 create mode 100644 .gitmodules
 create mode 160000 plastimatch

diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..fb13e0f
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "plastimatch"]
+	path = plastimatch
+	url = https://gitlab.com/plastimatch/plastimatch.git
diff --git a/plastimatch b/plastimatch
new file mode 160000
index 0000000..5036f97
--- /dev/null
+++ b/plastimatch
@@ -0,0 +1 @@
+Subproject commit 5036f97b213d37a0a07dd232c827fb5f35049ae4

From ee4d8c454272481051508efa1c0f0714526ccf44 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Mon, 20 Jan 2025 15:57:53 -0500
Subject: [PATCH 02/22] trying setup a clean docker file and installation
 script

---
 .gitignore                      |  1 +
 dockerfiles/.dockerignore       |  3 +++
 dockerfiles/Dockerfile          | 14 ++++++++++----
 dockerfiles/command_docker.sh   |  7 +++++++
 dockerfiles/docker-compose.yaml | 15 +++++++++++++++
 plastimatch                     |  1 -
 pyplastimatch/pyplastimatch.py  | 17 +++++++++++++++++
 7 files changed, 53 insertions(+), 5 deletions(-)
 create mode 100644 dockerfiles/.dockerignore
 create mode 100644 dockerfiles/command_docker.sh
 create mode 100644 dockerfiles/docker-compose.yaml
 delete mode 160000 plastimatch

diff --git a/.gitignore b/.gitignore
index 1ff31a5..7373cf4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
+plastimatch-ubuntu_24_04
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
diff --git a/dockerfiles/.dockerignore b/dockerfiles/.dockerignore
new file mode 100644
index 0000000..9d5f649
--- /dev/null
+++ b/dockerfiles/.dockerignore
@@ -0,0 +1,3 @@
+.trunk
+.git
+*build
diff --git a/dockerfiles/Dockerfile b/dockerfiles/Dockerfile
index 464a852..3ad2dc3 100644
--- a/dockerfiles/Dockerfile
+++ b/dockerfiles/Dockerfile
@@ -1,4 +1,4 @@
-from ubuntu:22.04
+FROM ubuntu:latest
 
 RUN apt-get update && apt-get install -y \
     build-essential \
@@ -15,8 +15,14 @@ RUN apt-get update && apt-get install -y \
     wget \
     && rm -rf /var/lib/apt/lists/*
 
-RUN pip install pyplastimatch
-RUN python3 -c 'from pyplastimatch.utils.install import install_precompiled_binaries; install_precompiled_binaries()'
+RUN apt-get install -y g++ make git cmake-curses-gui \
+    libblas-dev liblapack-dev libsqlite3-dev \
+    libdcmtk-dev libdlib-dev libfftw3-dev \
+    libinsighttoolkit5-dev \
+    libpng-dev libtiff-dev uuid-dev zlib1g-dev
+# RUN apt-get install pipx
+RUN pip3 install --break-system-packages pyplastimatch
+# RUN python3 -c 'from pyplastimatch.utils.install import install_precompiled_binaries; install_precompiled_binaries()'
 
-ENTRYPOINT ["plastimatch"]
+# ENTRYPOINT ["plastimatch"]
 
diff --git a/dockerfiles/command_docker.sh b/dockerfiles/command_docker.sh
new file mode 100644
index 0000000..dcd25a8
--- /dev/null
+++ b/dockerfiles/command_docker.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+# to build the image and run the container
+docker compose up --build -d
+# to run the container without building the image
+# docker compose up --no-build -d
+# to enter the container
+docker exec -it BrachyUtils bash
diff --git a/dockerfiles/docker-compose.yaml b/dockerfiles/docker-compose.yaml
new file mode 100644
index 0000000..049d3e3
--- /dev/null
+++ b/dockerfiles/docker-compose.yaml
@@ -0,0 +1,15 @@
+services:
+  PyPlastimatch:
+    build:
+      context: ../
+      dockerfile: dockerfiles/Dockerfile
+    image: pyplastimatch:latest
+    container_name: PyPlastimatch
+    stdin_open: true # docker run -i
+    tty: true # docker run -t
+    environment:
+      - HOST_HOME=${HOST_HOME}
+      - DEBIAN_FRONTEND=noninteractive
+    volumes:
+      - ../:/root/Software/pyplastimatch
+      - ${HOST_HOME}:/root/YourLocalHome
\ No newline at end of file
diff --git a/plastimatch b/plastimatch
deleted file mode 160000
index 5036f97..0000000
--- a/plastimatch
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 5036f97b213d37a0a07dd232c827fb5f35049ae4
diff --git a/pyplastimatch/pyplastimatch.py b/pyplastimatch/pyplastimatch.py
index 53693c2..9626733 100644
--- a/pyplastimatch/pyplastimatch.py
+++ b/pyplastimatch/pyplastimatch.py
@@ -16,6 +16,7 @@
 import json
 import subprocess
 from typing import Dict
+from pathlib import Path
 
 ## ----------------------------------------
 
@@ -282,3 +283,19 @@ def compare(path_to_reference_img, path_to_test_img, verbose = True) -> Dict[str
   return comparison_dict
 
 ## ----------------------------------------
+
+def register(
+  pth_fixed: Path | str, 
+  pth_moving: Path | str,
+  pth_fixed_roi: Path | str = None,
+  pth_moving_roi: Path | str = None,
+  fixed_landmarks: Path | str = None,
+  moving_landmarks: Path | str = None,
+  warped_landmarks: Path | str = None,
+  xform_in
+  verbose = True,
+  ) -> Dict[str, float]:
+  """
+  Purpose:
+      To register two images using the plastimatch register command.
+  """
\ No newline at end of file

From 56b1c0b7e51de133fdb8f6700125d329a7ac97f1 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Mon, 20 Jan 2025 16:14:20 -0500
Subject: [PATCH 03/22] renamed docker folder

---
 {dockerfiles => docker_src}/.dockerignore       | 0
 {dockerfiles => docker_src}/Dockerfile          | 0
 {dockerfiles => docker_src}/command_docker.sh   | 0
 {dockerfiles => docker_src}/docker-compose.yaml | 0
 4 files changed, 0 insertions(+), 0 deletions(-)
 rename {dockerfiles => docker_src}/.dockerignore (100%)
 rename {dockerfiles => docker_src}/Dockerfile (100%)
 rename {dockerfiles => docker_src}/command_docker.sh (100%)
 rename {dockerfiles => docker_src}/docker-compose.yaml (100%)

diff --git a/dockerfiles/.dockerignore b/docker_src/.dockerignore
similarity index 100%
rename from dockerfiles/.dockerignore
rename to docker_src/.dockerignore
diff --git a/dockerfiles/Dockerfile b/docker_src/Dockerfile
similarity index 100%
rename from dockerfiles/Dockerfile
rename to docker_src/Dockerfile
diff --git a/dockerfiles/command_docker.sh b/docker_src/command_docker.sh
similarity index 100%
rename from dockerfiles/command_docker.sh
rename to docker_src/command_docker.sh
diff --git a/dockerfiles/docker-compose.yaml b/docker_src/docker-compose.yaml
similarity index 100%
rename from dockerfiles/docker-compose.yaml
rename to docker_src/docker-compose.yaml

From 1258c08339b40c71c8094a734eb760969d6ac0e3 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Mon, 20 Jan 2025 17:00:38 -0500
Subject: [PATCH 04/22] got the image bulding to work. plastimatch command runs
 on the cli. it is to be tested from inside the python

---
 docker_src/Dockerfile          |  6 ++----
 docker_src/command_docker.sh   |  6 +++---
 docker_src/docker-compose.yaml |  2 +-
 pyplastimatch/pyplastimatch.py | 19 +++++++++++++++++--
 4 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/docker_src/Dockerfile b/docker_src/Dockerfile
index 3ad2dc3..3164f8e 100644
--- a/docker_src/Dockerfile
+++ b/docker_src/Dockerfile
@@ -12,11 +12,9 @@ RUN apt-get update && apt-get install -y \
     python3-pip \
     python3-setuptools \
     python3-wheel \
-    wget \
-    && rm -rf /var/lib/apt/lists/*
+    wget
 
-RUN apt-get install -y g++ make git cmake-curses-gui \
-    libblas-dev liblapack-dev libsqlite3-dev \
+RUN apt-get install -y g++ make git \
     libdcmtk-dev libdlib-dev libfftw3-dev \
     libinsighttoolkit5-dev \
     libpng-dev libtiff-dev uuid-dev zlib1g-dev
diff --git a/docker_src/command_docker.sh b/docker_src/command_docker.sh
index dcd25a8..397a2d8 100644
--- a/docker_src/command_docker.sh
+++ b/docker_src/command_docker.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 # to build the image and run the container
-docker compose up --build -d
+# docker compose up --build -d
 # to run the container without building the image
-# docker compose up --no-build -d
+docker compose up --no-build -d
 # to enter the container
-docker exec -it BrachyUtils bash
+docker exec -it PyPlastimatch bash
diff --git a/docker_src/docker-compose.yaml b/docker_src/docker-compose.yaml
index 049d3e3..7fb7587 100644
--- a/docker_src/docker-compose.yaml
+++ b/docker_src/docker-compose.yaml
@@ -2,7 +2,7 @@ services:
   PyPlastimatch:
     build:
       context: ../
-      dockerfile: dockerfiles/Dockerfile
+      dockerfile: docker_src/Dockerfile
     image: pyplastimatch:latest
     container_name: PyPlastimatch
     stdin_open: true # docker run -i
diff --git a/pyplastimatch/pyplastimatch.py b/pyplastimatch/pyplastimatch.py
index 9626733..75534c1 100644
--- a/pyplastimatch/pyplastimatch.py
+++ b/pyplastimatch/pyplastimatch.py
@@ -292,10 +292,25 @@ def register(
   fixed_landmarks: Path | str = None,
   moving_landmarks: Path | str = None,
   warped_landmarks: Path | str = None,
-  xform_in
+  xform_in: str = None,
+  xform_out: str = None,
+  vf_out: str = None,
+  img_out: Path | str = None,
+  img_out_fmt: str = "auto",
+  img_out_type: str = "auto",
+  resample_when_linear: bool = True,
+  logfile: Path | str = None,
   verbose = True,
   ) -> Dict[str, float]:
   """
   Purpose:
       To register two images using the plastimatch register command.
-  """
\ No newline at end of file
+  """
+  
+  
+  def test(a , b, **kwargs):
+    print(a, b)
+    myj = load_defaulat_json()
+    for key, val in kwargs.items():
+      if  
+      myj[key] = val

From 3da672b39a64d6f87b9574f7487f16b1a7ac313c Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Tue, 21 Jan 2025 11:03:01 -0500
Subject: [PATCH 05/22] made some slolid progress on the registration. we ge
 the input now, let's finish calling plastimatch

---
 pyplastimatch/pyplastimatch.py | 133 ++++++++++++++++++++++++++-------
 1 file changed, 107 insertions(+), 26 deletions(-)

diff --git a/pyplastimatch/pyplastimatch.py b/pyplastimatch/pyplastimatch.py
index 75534c1..a12b887 100644
--- a/pyplastimatch/pyplastimatch.py
+++ b/pyplastimatch/pyplastimatch.py
@@ -15,9 +15,9 @@
 import os
 import json
 import subprocess
-from typing import Dict
+from typing import Dict, List
 from pathlib import Path
-
+from collections import defaultdict
 ## ----------------------------------------
 
 # FIXME: like this, every command is basically the same function with a line changed
@@ -285,32 +285,113 @@ def compare(path_to_reference_img, path_to_test_img, verbose = True) -> Dict[str
 ## ----------------------------------------
 
 def register(
-  pth_fixed: Path | str, 
-  pth_moving: Path | str,
-  pth_fixed_roi: Path | str = None,
-  pth_moving_roi: Path | str = None,
-  fixed_landmarks: Path | str = None,
-  moving_landmarks: Path | str = None,
-  warped_landmarks: Path | str = None,
-  xform_in: str = None,
-  xform_out: str = None,
-  vf_out: str = None,
-  img_out: Path | str = None,
-  img_out_fmt: str = "auto",
-  img_out_type: str = "auto",
-  resample_when_linear: bool = True,
-  logfile: Path | str = None,
-  verbose = True,
+  global_params: Dict[str, str],
+  stage_params_list: List[Dict[str, str]]
   ) -> Dict[str, float]:
   """
   Purpose:
-      To register two images using the plastimatch register command.
+    - To register two images using the plastimatch register command. The input to the command is a 
+    text file called parm.txt. This text file has [Global] commands and [Stage] commands.
+    While the variables for the global commands stay the same throughout many stages of the registration,
+    the stage commands can be different for each stage. For the full list of these variables
+    look at https://plastimatch.org/registration_command_file_reference.html.
+    Here is an example of the parm.txt file:
+      [GLOBAL]
+      fixed=t5.mha
+      moving=t0.mha
+      image_out=warped.mha
+      vf_out=deformation.nrrd
+
+      [STAGE]
+      xform=bspline
+      grid_spac=50 50 50
+
+      [STAGE]
+      grid_spac=20 20 20
+
+  Inputs:
+    - global_params: dict := a dictionary containing the global parameters for the registration.
+    The possible global parameters are:
+      - fixed: str := the path to the fixed image.
+      - moving: str := the path to the moving image.
+      - fixed_roi: str := the path to the fixed region of interest.
+      - moving_roi: str := the path to the moving region of interest.
+      - fixed_landmarks: str := the path to the fixed landmarks.
+      - moving_landmarks: str := the path to the moving landmarks.
+      - warped_landmarks: str := the path to the warped landmarks.
+      - xform_in: str := the path to the input transformation.
+      - xform_out: str := the path to the output transformation.
+      - vf_out: str := the path to the output vector field.
+      - img_out: str := the path to the output image.
+      - img_out_fmt: str := the format of the output image.
+      - img_out_type: str := the type of the output image.
+      - resample_when_linear: bool := whether to resample when linear.
+      - logfile: str := the path to the log file.
+    - stage_params_list: List[Dict[str, str]] := a list of dictionaries containing the stage parameters for the registration.
+    please look at the plastimatch documentation for the full list of possible stage parameters.
+  Outputs:
+    - registration_summary: Dict[str, float] := a dictionary containing the registration summary.
+    The possible keys are:
+      - pth_registered_data: str := the path to the registered data.
+      - log_file: str := the path to the log file.
   """
   
-  
-  def test(a , b, **kwargs):
-    print(a, b)
-    myj = load_defaulat_json()
-    for key, val in kwargs.items():
-      if  
-      myj[key] = val
+  # here are the possible global parameters for the registration
+  # some are optional, some are mandatory, we loop through them 
+  # and create the command
+  global_param_possible_key_list = [
+    "fixed", "moving", "fixed_roi",
+    "moving_roi", "fixed_landmarks",
+    "moving_landmarks","warped_landmarks",
+    "xform_in", "xform_out", "vf_out",
+    "img_out", "img_out_fmt", "img_out_type",
+    "resample_when_linear", "logfile"
+  ]
+  final_global_params = defaultdict(str)
+  # loop through the global parameters and create the command
+  for key in global_params:
+    if key in global_param_possible_key_list:
+      final_global_params[key] = global_params[key]
+  
+  # make sure the required global parameters are present
+  if "fixed" not in final_global_params:
+    raise ValueError("The fixed image is required.")
+  if "moving" not in final_global_params:
+    raise ValueError("The moving image is required.")
+  if "image_out" not in final_global_params:
+    raise ValueError("The output image is required.")
+  
+  # here are the possible stage parameters for the registration
+  # some are optional, some are mandatory, we loop through them
+  # and create the command
+  stage_param_possible_key_list = [
+  "fixed_landmarks", "moving_landmarks", "warped_landmarks", "xform_out",
+  "vf_out", "img_out", "img_out_fmt", "img_out_type",
+  "resample_when_linear", "background_max", "convergence_tol", "default_value", 
+  "demons_acceleration", "demons_filter_width", "demons_homogenization", "demons_std", 
+  "demons_gradient_type", "demons_smooth_update_field", "demons_std_update_field",
+  "demons_smooth_deformation_field", "demons_std_deformation_field", "demons_step_length",
+  "grad_tol", "grid_spac", "gridsearch_min_overlap", "histoeq", "landmark_stiffness",
+  "lbfgsb_mmax", "mattes_fixed_minVal", "mattes_fixed_maxVal", "mattes_moving_minVal",
+  "mattes_moving_maxVal", "max_its", "max_step", "metric", "mi_histogram_bins", "min_its",
+  "min_step", "num_hist_levels_equal", "num_matching_points", "num_samples", "num_samples_pct",
+  "num_substages", "optim_subtype", "pgtol", "regularization", "diffusion_penalty", 
+  "curvature_penalty", "linear_elastic_multiplier", "third_order_penalty", 
+  "total_displacement_penalty", "lame_coefficient_1", "lame_coefficient_2", "res",
+  "res_mm", "res_mm_fixed", "res_mm_moving", "res_vox", "res_vox_fixed",
+  "res_vox_moving", "rsg_grad_tol", "ss", "ss_fixed", "ss_moving",
+  "threading", "thresh_mean_intensity", "translation_scale_factor",
+  ]
+  # loop through the stage parameters and create the command for each stage
+  final_stage_params_list = []
+  for stage_params in stage_params_list:
+    final_stage_params = defaultdict(str)
+    for key in stage_params:
+      if key in stage_param_possible_key_list:
+        final_stage_params[key] = stage_params[key]
+    final_stage_params_list.append(final_stage_params) 
+
+  # create the parm.txt file in the same directory as image_out
+  out_dir = Path(final_global_params["image_out"]).parent
+  parm_txt_path = out_dir.joinpath("parm.txt")
+  
\ No newline at end of file

From 9a56389f46102c31053d950ddd8e1b270880edbf Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Tue, 21 Jan 2025 11:53:13 -0500
Subject: [PATCH 06/22] put down the draft way to call register on plasti
 match. let's test it now

---
 pyplastimatch/pyplastimatch.py       | 21 +++++++++++++++++++--
 pyplastimatch/tests/__init__.py      |  0
 pyplastimatch/tests/test_register.py | 12 ++++++++++++
 3 files changed, 31 insertions(+), 2 deletions(-)
 create mode 100644 pyplastimatch/tests/__init__.py
 create mode 100644 pyplastimatch/tests/test_register.py

diff --git a/pyplastimatch/pyplastimatch.py b/pyplastimatch/pyplastimatch.py
index a12b887..3161c91 100644
--- a/pyplastimatch/pyplastimatch.py
+++ b/pyplastimatch/pyplastimatch.py
@@ -352,7 +352,7 @@ def register(
   for key in global_params:
     if key in global_param_possible_key_list:
       final_global_params[key] = global_params[key]
-  
+
   # make sure the required global parameters are present
   if "fixed" not in final_global_params:
     raise ValueError("The fixed image is required.")
@@ -394,4 +394,21 @@ def register(
   # create the parm.txt file in the same directory as image_out
   out_dir = Path(final_global_params["image_out"]).parent
   parm_txt_path = out_dir.joinpath("parm.txt")
-  
\ No newline at end of file
+  param_txt = "[Global]\n"
+  for key in final_global_params:
+    param_txt += f"{key}={final_global_params[key]}\n"
+  param_txt += "\n"
+  for stage in final_stage_params_list:
+    param_txt += "[Stage]\n"
+    for key in stage:
+      param_txt += f"{key}={stage[key]}\n"
+    param_txt += "\n"
+
+  with open(parm_txt_path, "w") as f:
+    f.write(param_txt)
+  
+  command = ["plastimatch", "register", str(parm_txt_path)]
+  try:
+    registration_summary = subprocess.run(command, capture_output = True, check = True)
+  except Exception as e:
+    print(e)
diff --git a/pyplastimatch/tests/__init__.py b/pyplastimatch/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/pyplastimatch/tests/test_register.py b/pyplastimatch/tests/test_register.py
new file mode 100644
index 0000000..6cdd671
--- /dev/null
+++ b/pyplastimatch/tests/test_register.py
@@ -0,0 +1,12 @@
+from PyPlastimatch import register
+
+def test_register():
+    pth_static = ""
+    pth_moving = ""
+    pth_output = ""
+    
+    global_params = {
+        "fixed" : f"{pth_static}",
+        "moving" : f"{pth_moving}",
+        "img_out" : f"{pth_output}",
+    }

From a0ea798ee3793cdaa4b801ecea273a7e68e8f425 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Tue, 21 Jan 2025 11:58:10 -0500
Subject: [PATCH 07/22] downloaded the sample data for testing of pyplastimatch

---
 .gitignore         | 3 +++
 data_test/.gitkeep | 0
 2 files changed, 3 insertions(+)
 create mode 100644 data_test/.gitkeep

diff --git a/.gitignore b/.gitignore
index 7373cf4..1ab2bcd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,6 @@
+data_test/*
+!data_test/.gitkeep
+
 plastimatch-ubuntu_24_04
 # Byte-compiled / optimized / DLL files
 __pycache__/
diff --git a/data_test/.gitkeep b/data_test/.gitkeep
new file mode 100644
index 0000000..e69de29

From 81d184547060b448e58d6adf17504a7183b148e9 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Tue, 21 Jan 2025 13:21:59 -0500
Subject: [PATCH 08/22] wrote the first test

---
 pyplastimatch/tests/test_register.py | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/pyplastimatch/tests/test_register.py b/pyplastimatch/tests/test_register.py
index 6cdd671..cd405f0 100644
--- a/pyplastimatch/tests/test_register.py
+++ b/pyplastimatch/tests/test_register.py
@@ -1,12 +1,22 @@
-from PyPlastimatch import register
+from pyplastimatch import register
 
 def test_register():
-    pth_static = ""
-    pth_moving = ""
-    pth_output = ""
-    
+    pth_static = "../data_test/registration-tutorial/t5.mha"
+    pth_moving = "../data_test/registration-tutorial/t0.mha"
+    pth_output = "../data_test/test_output/registered.nrrd"
+
     global_params = {
         "fixed" : f"{pth_static}",
         "moving" : f"{pth_moving}",
         "img_out" : f"{pth_output}",
     }
+    
+    stage_params_list = [
+        {
+            "xform": "bspline"
+        }
+    ]
+    register(global_params, stage_params)
+
+if __name__ == "__main__":
+    test_register()
\ No newline at end of file

From 3fe25163bb8cbd2867b252f9e02613e0bc1caeb5 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Tue, 21 Jan 2025 13:40:12 -0500
Subject: [PATCH 09/22] runnign registration worked for the basic example case

---
 docker_src/Dockerfile                | 11 ++++++-----
 pyplastimatch/pyplastimatch.py       |  5 +++--
 pyplastimatch/tests/test_register.py |  4 ++--
 3 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/docker_src/Dockerfile b/docker_src/Dockerfile
index 3164f8e..62dd5d2 100644
--- a/docker_src/Dockerfile
+++ b/docker_src/Dockerfile
@@ -12,12 +12,13 @@ RUN apt-get update && apt-get install -y \
     python3-pip \
     python3-setuptools \
     python3-wheel \
-    wget
-
-RUN apt-get install -y g++ make git \
-    libdcmtk-dev libdlib-dev libfftw3-dev \
+    wget libdcmtk-dev libdlib-dev libfftw3-dev \
     libinsighttoolkit5-dev \
-    libpng-dev libtiff-dev uuid-dev zlib1g-dev
+    libpng-dev libtiff-dev uuid-dev zlib1g-dev \
+    plastimatch && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
 # RUN apt-get install pipx
 RUN pip3 install --break-system-packages pyplastimatch
 # RUN python3 -c 'from pyplastimatch.utils.install import install_precompiled_binaries; install_precompiled_binaries()'
diff --git a/pyplastimatch/pyplastimatch.py b/pyplastimatch/pyplastimatch.py
index 3161c91..78e4c46 100644
--- a/pyplastimatch/pyplastimatch.py
+++ b/pyplastimatch/pyplastimatch.py
@@ -344,7 +344,7 @@ def register(
     "moving_roi", "fixed_landmarks",
     "moving_landmarks","warped_landmarks",
     "xform_in", "xform_out", "vf_out",
-    "img_out", "img_out_fmt", "img_out_type",
+    "image_out", "img_out_fmt", "img_out_type",
     "resample_when_linear", "logfile"
   ]
   final_global_params = defaultdict(str)
@@ -366,7 +366,7 @@ def register(
   # and create the command
   stage_param_possible_key_list = [
   "fixed_landmarks", "moving_landmarks", "warped_landmarks", "xform_out",
-  "vf_out", "img_out", "img_out_fmt", "img_out_type",
+  "xform", "vf_out", "img_out", "img_out_fmt", "img_out_type",
   "resample_when_linear", "background_max", "convergence_tol", "default_value", 
   "demons_acceleration", "demons_filter_width", "demons_homogenization", "demons_std", 
   "demons_gradient_type", "demons_smooth_update_field", "demons_std_update_field",
@@ -393,6 +393,7 @@ def register(
 
   # create the parm.txt file in the same directory as image_out
   out_dir = Path(final_global_params["image_out"]).parent
+  os.makedirs(out_dir, exist_ok=True)
   parm_txt_path = out_dir.joinpath("parm.txt")
   param_txt = "[Global]\n"
   for key in final_global_params:
diff --git a/pyplastimatch/tests/test_register.py b/pyplastimatch/tests/test_register.py
index cd405f0..4e7e82e 100644
--- a/pyplastimatch/tests/test_register.py
+++ b/pyplastimatch/tests/test_register.py
@@ -8,7 +8,7 @@ def test_register():
     global_params = {
         "fixed" : f"{pth_static}",
         "moving" : f"{pth_moving}",
-        "img_out" : f"{pth_output}",
+        "image_out" : f"{pth_output}",
     }
     
     stage_params_list = [
@@ -16,7 +16,7 @@ def test_register():
             "xform": "bspline"
         }
     ]
-    register(global_params, stage_params)
+    register(global_params, stage_params_list)
 
 if __name__ == "__main__":
     test_register()
\ No newline at end of file

From b04c7d9e15a9d7617c23e501b28b34fcaf8db754 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Tue, 21 Jan 2025 17:12:59 -0500
Subject: [PATCH 10/22] just organized the docker file a bit better

---
 docker_src/Dockerfile | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/docker_src/Dockerfile b/docker_src/Dockerfile
index 62dd5d2..99589b4 100644
--- a/docker_src/Dockerfile
+++ b/docker_src/Dockerfile
@@ -1,17 +1,11 @@
 FROM ubuntu:latest
 
 RUN apt-get update && apt-get install -y \
-    build-essential \
-    cmake \
-    git \
-    libboost-all-dev \
-    libssl-dev \
-    libzmq3-dev \
-    pkg-config \
-    python3 \
-    python3-pip \
-    python3-setuptools \
-    python3-wheel \
+    build-essential cmake git \
+    libboost-all-dev libssl-dev \
+    libzmq3-dev pkg-config \
+    python3 python3-pip \
+    python3-setuptools python3-wheel \
     wget libdcmtk-dev libdlib-dev libfftw3-dev \
     libinsighttoolkit5-dev \
     libpng-dev libtiff-dev uuid-dev zlib1g-dev \

From a32c97b86dd3c764324ebb9b098c35e43845a661 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Wed, 22 Jan 2025 08:08:17 -0500
Subject: [PATCH 11/22] wrote a simple api for registration

---
 .gitignore         |  3 ++-
 pyplsti_api.py     | 41 +++++++++++++++++++++++++++++++++++++++++
 temp_data/.gitkeep |  0
 3 files changed, 43 insertions(+), 1 deletion(-)
 create mode 100644 pyplsti_api.py
 create mode 100644 temp_data/.gitkeep

diff --git a/.gitignore b/.gitignore
index 1ab2bcd..8c17385 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,7 @@
 data_test/*
 !data_test/.gitkeep
-
+temp_data/*
+!temp_data/.gitkeep
 plastimatch-ubuntu_24_04
 # Byte-compiled / optimized / DLL files
 __pycache__/
diff --git a/pyplsti_api.py b/pyplsti_api.py
new file mode 100644
index 0000000..05b50b1
--- /dev/null
+++ b/pyplsti_api.py
@@ -0,0 +1,41 @@
+from fastapi import FastAPI, HTTPException
+from subprocess import Popen, PIPE, run
+# from fastapi import FastAPI
+# from fastapi.responses import StreamingResponse
+
+
+import subprocess
+import os
+from typing import Dict, List
+from pathlib import Path
+# from glob import glob
+# from collections import defaultdict
+# import json
+from pydantic import BaseModel, field_validator, Field
+
+from pyplastimatch import register
+
+class Inputs_register(BaseModel):
+    r"""
+    Purpose:
+        - To define the input parameters for running image registration using pyplastimatch.
+    Attributes:
+        - global_params: a dictionary containing the global parameters for the registration.
+        - stage_params_list: a list of dictionaries defining the parameters for each stage of the registration.
+        please consult pyplastimatch.register() documentation for more information.
+    """
+
+    global_params: Dict[str, str]
+    stage_params_list: List[Dict[str, str]]
+
+app = FastAPI()
+
+@app.post("/register")
+def register(
+    all_inputs: Inputs_register
+    ) -> None:
+    r"""
+    Purpose:
+        - To run image registration using pyplastimatch.
+    """
+    register(all_inputs.global_params, all_inputs.stage_params_list)
\ No newline at end of file
diff --git a/temp_data/.gitkeep b/temp_data/.gitkeep
new file mode 100644
index 0000000..e69de29

From 7659a4b0c1b5dae4d25f6e7a6248289e8825b522 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Wed, 22 Jan 2025 08:38:35 -0500
Subject: [PATCH 12/22] wrote a bash script to run the api

---
 run_api.sh | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 run_api.sh

diff --git a/run_api.sh b/run_api.sh
new file mode 100644
index 0000000..5513825
--- /dev/null
+++ b/run_api.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+fastapi run ${HOME}/Software/pyplastimatch/pyplsti_api.py > /var/log/pyplastimatch.log

From 467221b2940a79c688136fd74404c4b7bd99303b Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Wed, 22 Jan 2025 11:49:03 -0500
Subject: [PATCH 13/22] updated the input model in the api to handle paths to
 the temp_data

---
 pyplsti_api.py | 35 ++++++++++++++++++++++++++++++++---
 1 file changed, 32 insertions(+), 3 deletions(-)

diff --git a/pyplsti_api.py b/pyplsti_api.py
index 05b50b1..3041834 100644
--- a/pyplsti_api.py
+++ b/pyplsti_api.py
@@ -27,15 +27,44 @@ class Inputs_register(BaseModel):
 
     global_params: Dict[str, str]
     stage_params_list: List[Dict[str, str]]
+    def __init__(self, **data):
+        super().__init__(**data)
+        dir_temp_data = Path(__file__).parent.joinpath("temp_data")
+        self.global_params["fixed"] = dir_temp_data.joinpath(self.global_params.get("fixed"))
+        self.global_params["moving"] = dir_temp_data.joinpath(self.global_params.get("moving"))
+        self.global_params["image_out"] = dir_temp_data.joinpath(self.global_params.get("image_out"))
 
 app = FastAPI()
 
-@app.post("/register")
-def register(
+@app.post("/plastimatch_register")
+def register_api(
     all_inputs: Inputs_register
     ) -> None:
     r"""
     Purpose:
         - To run image registration using pyplastimatch.
     """
-    register(all_inputs.global_params, all_inputs.stage_params_list)
\ No newline at end of file
+    register(all_inputs.global_params, all_inputs.stage_params_list)
+
+
+def test_register_api():
+    pth_static = "static.nrrd"
+    pth_moving = "moving.nrrd"
+    pth_output = "registered.nrrd"
+
+    global_params = {
+        "fixed" : f"{pth_static}",
+        "moving" : f"{pth_moving}",
+        "image_out" : f"{pth_output}",
+    }
+    
+    stage_params_list = [
+        {
+            "xform": "bspline"
+        }
+    ]
+    inputs = Inputs_register(global_params=global_params, stage_params_list=stage_params_list)
+    register_api(inputs)
+
+if __name__ == "__main__":
+    test_register_api()
\ No newline at end of file

From a9b460c1f5241fbf07b59705abb66cd2e617bb44 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Thu, 23 Jan 2025 10:48:17 -0500
Subject: [PATCH 14/22] added some print statement for the logs!

---
 pyplsti_api.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyplsti_api.py b/pyplsti_api.py
index 3041834..916598a 100644
--- a/pyplsti_api.py
+++ b/pyplsti_api.py
@@ -44,6 +44,9 @@ def register_api(
     Purpose:
         - To run image registration using pyplastimatch.
     """
+    print(f"static image: {all_inputs.global_params['fixed']}")
+    print(f"moving image: {all_inputs.global_params['moving']}")
+    print(f"output image: {all_inputs.global_params['image_out']}")
     register(all_inputs.global_params, all_inputs.stage_params_list)
 
 

From 6508b187f6fc556cb4fe2237ee9ec660703e2e93 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Thu, 23 Jan 2025 11:26:05 -0500
Subject: [PATCH 15/22] put a .env file that helps out docker compose with
 environment variables

---
 .gitignore      | 1 +
 docker_src/.env | 1 +
 2 files changed, 2 insertions(+)
 create mode 100644 docker_src/.env

diff --git a/.gitignore b/.gitignore
index 8c17385..be824cd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -108,6 +108,7 @@ celerybeat.pid
 
 # Environments
 .env
+!docker_src/.env
 .venv
 env/
 venv/
diff --git a/docker_src/.env b/docker_src/.env
new file mode 100644
index 0000000..74eaf50
--- /dev/null
+++ b/docker_src/.env
@@ -0,0 +1 @@
+HOST_HOME=${HOME}
\ No newline at end of file

From 81bdca7016b9de20d73598949513ab6a2c7d8e33 Mon Sep 17 00:00:00 2001
From: hosseinjafar <43022986+hosseinjafar@users.noreply.github.com>
Date: Sat, 25 Jan 2025 07:59:45 -0500
Subject: [PATCH 16/22] Update README.md

renamed dockerfiles with docker_src since this folder contains more than dockerfile.
---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 9b155e8..70452fe 100644
--- a/README.md
+++ b/README.md
@@ -94,14 +94,14 @@ Note: provided you have a Google Cloud Platform project correctly set up, you wi
 
 # Ubuntu 22.04 LTS Plastimatch Docker Container
 
-If you want to test Plastimatch for Ubuntu 22.04 LTS, you can use the Docker image we shared for this purpose under `dockerfiles`.
+If you want to test Plastimatch for Ubuntu 22.04 LTS, you can use the Docker image we shared for this purpose under `docker_src`.
 
 ## Build the Docker Container
 
 To build the Ubuntu 22.04 LTS Platimatch Docker container, run the following commands from the root of the PyPlastimatch repository:
 
 ```
-cd dockerfiles/
+cd docker_src/
 
 docker build --tag pypla_22.04 . --no-cache
 ```

From 93410c5a13b896b44cfc18e06186141260d2d0b5 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Thu, 13 Feb 2025 11:08:25 -0500
Subject: [PATCH 17/22] exporing transforms as nrrd

---
 pyplsti_api.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyplsti_api.py b/pyplsti_api.py
index 916598a..a16752b 100644
--- a/pyplsti_api.py
+++ b/pyplsti_api.py
@@ -33,6 +33,7 @@ def __init__(self, **data):
         self.global_params["fixed"] = dir_temp_data.joinpath(self.global_params.get("fixed"))
         self.global_params["moving"] = dir_temp_data.joinpath(self.global_params.get("moving"))
         self.global_params["image_out"] = dir_temp_data.joinpath(self.global_params.get("image_out"))
+        self.global_params["vf_out"] = dir_temp_data.joinpath(self.global_params.get("vf_out"))
 
 app = FastAPI()
 
@@ -47,9 +48,9 @@ def register_api(
     print(f"static image: {all_inputs.global_params['fixed']}")
     print(f"moving image: {all_inputs.global_params['moving']}")
     print(f"output image: {all_inputs.global_params['image_out']}")
+    print(f"output vf: {all_inputs.global_params['vf_out']}")
     register(all_inputs.global_params, all_inputs.stage_params_list)
 
-
 def test_register_api():
     pth_static = "static.nrrd"
     pth_moving = "moving.nrrd"

From 0c7d8c889af0c50eef4d296a371f9dcdf6654812 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Wed, 26 Feb 2025 14:29:23 -0500
Subject: [PATCH 18/22] made a bunch of changes to work with convert over the
 api. the changes include:\n 1. replacing _ with - in the inputs for the
 convert command.\n 2. automatically removing \temp\ temp_data/ from all the
 inputs and adding the correct path for temp_data. implementing the api call
 for conver

---
 pyplastimatch/pyplastimatch.py |   4 +-
 pyplsti_api.py                 | 108 +++++++++++++++++++++++++++------
 2 files changed, 91 insertions(+), 21 deletions(-)

diff --git a/pyplastimatch/pyplastimatch.py b/pyplastimatch/pyplastimatch.py
index 78e4c46..da11038 100644
--- a/pyplastimatch/pyplastimatch.py
+++ b/pyplastimatch/pyplastimatch.py
@@ -45,8 +45,10 @@ def convert(verbose = True, path_to_log_file = None, return_bash_command = False
   bash_command += ["plastimatch", "convert"]
   
   for key, val in kwargs.items():
+    if "_" in key:
+      key = key.replace("_", "-")
     bash_command += ["--%s"%(key), val]
-  
+
   if verbose:
     print("\nRunning 'plastimatch convert' with the specified arguments:")
     for key, val in kwargs.items():
diff --git a/pyplsti_api.py b/pyplsti_api.py
index a16752b..813d4f3 100644
--- a/pyplsti_api.py
+++ b/pyplsti_api.py
@@ -15,11 +15,13 @@
 
 from pyplastimatch import register
 
+app = FastAPI()
+
 class Inputs_register(BaseModel):
     r"""
-    Purpose:
+    ### Purpose:
         - To define the input parameters for running image registration using pyplastimatch.
-    Attributes:
+    ### Attributes:
         - global_params: a dictionary containing the global parameters for the registration.
         - stage_params_list: a list of dictionaries defining the parameters for each stage of the registration.
         please consult pyplastimatch.register() documentation for more information.
@@ -30,38 +32,94 @@ class Inputs_register(BaseModel):
     def __init__(self, **data):
         super().__init__(**data)
         dir_temp_data = Path(__file__).parent.joinpath("temp_data")
-        self.global_params["fixed"] = dir_temp_data.joinpath(self.global_params.get("fixed"))
-        self.global_params["moving"] = dir_temp_data.joinpath(self.global_params.get("moving"))
-        self.global_params["image_out"] = dir_temp_data.joinpath(self.global_params.get("image_out"))
-        self.global_params["vf_out"] = dir_temp_data.joinpath(self.global_params.get("vf_out"))
-
-app = FastAPI()
+        for key, value in self.global_params.items():
+            if "temp_data/" in value:
+                value = value.split("temp_data/")[-1]
+            value = dir_temp_data.joinpath(value)
+            self.global_params[key] = value
 
 @app.post("/plastimatch_register")
 def register_api(
-    all_inputs: Inputs_register
+    all_registration_inputs: Inputs_register
     ) -> None:
     r"""
-    Purpose:
+    ### Purpose:
         - To run image registration using pyplastimatch.
+    
+    ### Inputs:
+        - all_registration_inputs: an instance of Inputs_register containing the input parameters for the registration.
+    """
+    print(f"static image: {all_registration_inputs.global_params['fixed']}")
+    print(f"moving image: {all_registration_inputs.global_params['moving']}")
+    print(f"output image: {all_registration_inputs.global_params['image_out']}")
+    print(f"output vf: {all_registration_inputs.global_params['vf_out']}")
+    register(all_registration_inputs.global_params, all_registration_inputs.stage_params_list)
+
+class Inputs_convert(BaseModel):
+    r"""
+    ### Purpose:
+        - To define the input parameters for running the convert command of pyplastimatch.
+    
+    ### Attributes:
+        - options: a dictionary containing the options for the convert command.
+        - input_file: the input file for the convert command.
+    """
+    pth_input: Path | str = None
+    pth_output: Path | str = None
+    options: Dict[str, str] = None
+
+    # these attributes will be filled from the options
+    xf: Path | str = None
+
+    def __init__(self, **data):
+        dir_temp_data = Path(__file__).parent.joinpath("temp_data")
+        for key, value in data.items():
+            if isinstance(value, str):
+                if "temp_data/" in value:
+                    value = value.split("temp_data/")[-1]
+                value = dir_temp_data.joinpath(value)
+            if key == "options":
+                for key_opt, value_opt in value.items():
+                    if "temp_data/" in value_opt:
+                        value_opt = value_opt.split("temp_data/")[-1]
+                    value[key_opt] = dir_temp_data.joinpath(value_opt)
+            data[key] = value
+
+        super().__init__()
+        self.pth_input = data.get("pth_input")
+        self.pth_output = data.get("pth_output")
+        self.xf = data.get("options").get("xf")
+
+@app.post("/plastimatch_convert")
+def convert_api(
+    all_convert_inputs: Inputs_convert
+    ) -> None:
+    r"""
+    ### Purpose:
+        - To run the convert command of pyplastimatch.
+    ### Inputs:
+        - all_convert_inputs: an instance of Inputs_convert containing the input parameters for the convert command.    
     """
-    print(f"static image: {all_inputs.global_params['fixed']}")
-    print(f"moving image: {all_inputs.global_params['moving']}")
-    print(f"output image: {all_inputs.global_params['image_out']}")
-    print(f"output vf: {all_inputs.global_params['vf_out']}")
-    register(all_inputs.global_params, all_inputs.stage_params_list)
+    from pyplastimatch import convert
+    convert(
+        input=all_convert_inputs.pth_input,
+        output_img=all_convert_inputs.pth_output,
+        xf=all_convert_inputs.xf
+    )
 
 def test_register_api():
-    pth_static = "static.nrrd"
-    pth_moving = "moving.nrrd"
-    pth_output = "registered.nrrd"
+    pth_static = "../temp_data/static.nrrd"
+    pth_moving = "../temp_data/moving.nrrd"
+    pth_output = "../temp_data/registered.nrrd"
+    vf_out = "../temp_data/vf.nrrd"
 
     global_params = {
         "fixed" : f"{pth_static}",
         "moving" : f"{pth_moving}",
         "image_out" : f"{pth_output}",
+        "vf_out" : f"{vf_out}",
     }
-    
+
     stage_params_list = [
         {
             "xform": "bspline"
@@ -70,5 +128,15 @@ def test_register_api():
     inputs = Inputs_register(global_params=global_params, stage_params_list=stage_params_list)
     register_api(inputs)
 
+def test_convert_api():
+    pth_input = "../temp_data/moving.nrrd"
+    pth_output = "../temp_data/warped.nrrd"
+    options = {
+        "xf": "vf.nrrd"
+    }
+    inputs = Inputs_convert(pth_input=pth_input, pth_output=pth_output, options=options)
+    convert_api(inputs)
+
 if __name__ == "__main__":
-    test_register_api()
\ No newline at end of file
+    # test_register_api()
+    test_convert_api()
\ No newline at end of file

From 695c4e81e483c871eceba5768aa94115d7650d18 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Wed, 26 Feb 2025 15:02:06 -0500
Subject: [PATCH 19/22] simplified the api and tested it over the web. good to
 go to the next stage

---
 pyplsti_api.py | 19 +++----------------
 run_api.sh     |  2 +-
 2 files changed, 4 insertions(+), 17 deletions(-)

diff --git a/pyplsti_api.py b/pyplsti_api.py
index 813d4f3..de9d107 100644
--- a/pyplsti_api.py
+++ b/pyplsti_api.py
@@ -66,8 +66,6 @@ class Inputs_convert(BaseModel):
     """
     pth_input: Path | str = None
     pth_output: Path | str = None
-    options: Dict[str, str] = None
-
     # these attributes will be filled from the options
     xf: Path | str = None
 
@@ -78,17 +76,8 @@ def __init__(self, **data):
                 if "temp_data/" in value:
                     value = value.split("temp_data/")[-1]
                 value = dir_temp_data.joinpath(value)
-            if key == "options":
-                for key_opt, value_opt in value.items():
-                    if "temp_data/" in value_opt:
-                        value_opt = value_opt.split("temp_data/")[-1]
-                    value[key_opt] = dir_temp_data.joinpath(value_opt)
             data[key] = value
-
-        super().__init__()
-        self.pth_input = data.get("pth_input")
-        self.pth_output = data.get("pth_output")
-        self.xf = data.get("options").get("xf")
+        super().__init__(**data)
 
 @app.post("/plastimatch_convert")
 def convert_api(
@@ -131,10 +120,8 @@ def test_register_api():
 def test_convert_api():
     pth_input = "../temp_data/moving.nrrd"
     pth_output = "../temp_data/warped.nrrd"
-    options = {
-        "xf": "vf.nrrd"
-    }
-    inputs = Inputs_convert(pth_input=pth_input, pth_output=pth_output, options=options)
+    xf = "../temp_data/vf.nrrd"
+    inputs = Inputs_convert(pth_input=pth_input, pth_output=pth_output, xf=xf)
     convert_api(inputs)
 
 if __name__ == "__main__":
diff --git a/run_api.sh b/run_api.sh
index 5513825..bc9644f 100644
--- a/run_api.sh
+++ b/run_api.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-fastapi run ${HOME}/Software/pyplastimatch/pyplsti_api.py > /var/log/pyplastimatch.log
+fastapi dev ${HOME}/Software/pyplastimatch/pyplsti_api.py > /var/log/pyplastimatch.log

From c411d5eda5ea2db604744aae9fadc0149e4e19a1 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Mon, 3 Mar 2025 15:58:00 -0500
Subject: [PATCH 20/22] very important bug fix. fastapi needs to be run with
 the run command and not the dev command for the other containers to notice it

---
 run_api.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/run_api.sh b/run_api.sh
index bc9644f..5513825 100644
--- a/run_api.sh
+++ b/run_api.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-fastapi dev ${HOME}/Software/pyplastimatch/pyplsti_api.py > /var/log/pyplastimatch.log
+fastapi run ${HOME}/Software/pyplastimatch/pyplsti_api.py > /var/log/pyplastimatch.log

From 8a74f8c59e35ccb681a51db1e9606eeb3de1e862 Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Wed, 16 Apr 2025 16:18:28 -0400
Subject: [PATCH 21/22] played with the temp file paths

---
 pyplastimatch/pyplastimatch.py | 2 +-
 pyplsti_api.py                 | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/pyplastimatch/pyplastimatch.py b/pyplastimatch/pyplastimatch.py
index da11038..c8e4421 100644
--- a/pyplastimatch/pyplastimatch.py
+++ b/pyplastimatch/pyplastimatch.py
@@ -377,7 +377,7 @@ def register(
   "lbfgsb_mmax", "mattes_fixed_minVal", "mattes_fixed_maxVal", "mattes_moving_minVal",
   "mattes_moving_maxVal", "max_its", "max_step", "metric", "mi_histogram_bins", "min_its",
   "min_step", "num_hist_levels_equal", "num_matching_points", "num_samples", "num_samples_pct",
-  "num_substages", "optim_subtype", "pgtol", "regularization", "diffusion_penalty", 
+  "num_substages","optim", "optim_subtype", "pgtol", "regularization", "diffusion_penalty", 
   "curvature_penalty", "linear_elastic_multiplier", "third_order_penalty", 
   "total_displacement_penalty", "lame_coefficient_1", "lame_coefficient_2", "res",
   "res_mm", "res_mm_fixed", "res_mm_moving", "res_vox", "res_vox_fixed",
diff --git a/pyplsti_api.py b/pyplsti_api.py
index de9d107..660c1ca 100644
--- a/pyplsti_api.py
+++ b/pyplsti_api.py
@@ -33,8 +33,8 @@ def __init__(self, **data):
         super().__init__(**data)
         dir_temp_data = Path(__file__).parent.joinpath("temp_data")
         for key, value in self.global_params.items():
-            if "temp_data/" in value:
-                value = value.split("temp_data/")[-1]
+            if "temp_data/registration/" in value:
+                value = value.split("temp_data/registration/")[-1]
             value = dir_temp_data.joinpath(value)
             self.global_params[key] = value
 
@@ -73,8 +73,8 @@ def __init__(self, **data):
         dir_temp_data = Path(__file__).parent.joinpath("temp_data")
         for key, value in data.items():
             if isinstance(value, str):
-                if "temp_data/" in value:
-                    value = value.split("temp_data/")[-1]
+                if "temp_data/registration/" in value:
+                    value = value.split("temp_data/registration/")[-1]
                 value = dir_temp_data.joinpath(value)
             data[key] = value
         super().__init__(**data)

From 43726dc1dc3c28deb308989330513597dc30c98d Mon Sep 17 00:00:00 2001
From: hosseinjafar <hosseinj.2555@gmail.com>
Date: Tue, 1 Jul 2025 16:51:33 -0400
Subject: [PATCH 22/22] simpler docker i guess

---
 docker_src/Dockerfile        | 6 +++---
 docker_src/command_docker.sh | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/docker_src/Dockerfile b/docker_src/Dockerfile
index 99589b4..55a9923 100644
--- a/docker_src/Dockerfile
+++ b/docker_src/Dockerfile
@@ -9,9 +9,9 @@ RUN apt-get update && apt-get install -y \
     wget libdcmtk-dev libdlib-dev libfftw3-dev \
     libinsighttoolkit5-dev \
     libpng-dev libtiff-dev uuid-dev zlib1g-dev \
-    plastimatch && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
+    plastimatch
+#    apt-get clean && \
+ #   rm -rf /var/lib/apt/lists/*
 
 # RUN apt-get install pipx
 RUN pip3 install --break-system-packages pyplastimatch
diff --git a/docker_src/command_docker.sh b/docker_src/command_docker.sh
index 397a2d8..eb5fa5b 100644
--- a/docker_src/command_docker.sh
+++ b/docker_src/command_docker.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 # to build the image and run the container
-# docker compose up --build -d
+docker compose up --build -d
 # to run the container without building the image
-docker compose up --no-build -d
+# docker compose up --no-build -d
 # to enter the container
 docker exec -it PyPlastimatch bash