Merge pull request #40 from tomography/win

Changes for windows
tomography · Jun 1, 2023 · 50ea2b7 · 50ea2b7
2 parents 0ff27a0 + 60ef946
commit 50ea2b7
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Showing 8 changed files with 28 additions and 33 deletions.
diff --git a/recipe/meta.yaml b/recipe/meta.yaml
@@ -39,8 +39,9 @@ requirements:
     - numexpr
     - numpy
     - opencv
+    - opencv-contrib-python
     - pywavelets
-    - tifffile
+    - tifffile    
 
 about:
     home: https://github.com/tomography/tomocupy

diff --git a/requirements.txt b/requirements.txt
diff --git a/src/cuda/CMakeLists.txt b/src/cuda/CMakeLists.txt
@@ -13,7 +13,6 @@ include_directories(${PYTHON_INCLUDE_PATH})
 # TODO: Is NumPy required?
 #find_package(NumPy REQUIRED)
 #include_directories(${NumPy_INCLUDE_DIRS})
-
 # Must tell CMake that SWIG interface files are CXX files
 
 set_source_files_properties(cfunc_fourierrec.i PROPERTIES CPLUSPLUS ON)

diff --git a/src/tomocupy/rec.py b/src/tomocupy/rec.py
@@ -70,7 +70,7 @@ def __init__(self, args):
 
         # Set ^C, ^Z interrupt to abort and deallocate memory on GPU
         signal.signal(signal.SIGINT, utils.signal_handler)
-        signal.signal(signal.SIGTSTP, utils.signal_handler)
+        signal.signal(signal.SIGTERM, utils.signal_handler)
 
         # configure sizes and output files
         cl_reader = reader.Reader(args)

diff --git a/src/tomocupy/rec_steps.py b/src/tomocupy/rec_steps.py
@@ -73,7 +73,7 @@ class GPURecSteps():
     def __init__(self, args):
         # Set ^C interrupt to abort and deallocate memory on GPU
         signal.signal(signal.SIGINT, utils.signal_handler)
-        signal.signal(signal.SIGTSTP, utils.signal_handler)
+        signal.signal(signal.SIGTERM, utils.signal_handler)
 
         # configure sizes and output files
         cl_reader = reader.Reader(args)

diff --git a/src/tomocupy/writer.py b/src/tomocupy/writer.py
@@ -84,7 +84,8 @@ def init_output_files_try(self):
                 self.args.file_name)+'_rec/try_center/'+os.path.basename(self.args.file_name)[:-3]
         else:
             fnameout = str(self.args.out_path_name)            
-        os.system(f'mkdir -p {fnameout}')
+        if not os.path.exists(fnameout):
+            os.makedirs(fnameout)
         fnameout += '/recon'
         self.fnameout = fnameout
         if (self.args.clear_folder=='True'):
@@ -101,8 +102,9 @@ def init_output_files(self):
                 self.args.file_name)+'_rec/'+os.path.basename(self.args.file_name)[:-3]+'_rec'            
         else:
             fnameout = str(self.args.out_path_name)
-        os.system(f'mkdir -p {fnameout}')
-
+        if not os.path.exists(fnameout):
+            os.makedirs(fnameout)
+
         if (self.args.clear_folder=='True'):
             log.info('Clearing the output folder')
             os.system(f'rm {fnameout}/*')
@@ -122,8 +124,9 @@ def init_output_files(self):
             fnameout += '.h5'
             # Assemble virtual dataset
             layout = h5py.VirtualLayout(shape=(
-                self.nzi/2**self.args.binning, self.n, self.n), dtype=self.dtype)
-            os.system(f'mkdir -p {fnameout[:-3]}_parts')
+                self.nzi/2**self.args.binning, self.n, self.n), dtype=self.dtype)            
+            if not os.path.exists(f'{fnameout[:-3]}_parts'):
+                os.makedirs(f'{fnameout[:-3]}_parts')
             for k in range(self.nzchunk):
                 filename = f"{fnameout[:-3]}_parts/p{k:04d}.h5"
                 vsource = h5py.VirtualSource(
@@ -181,7 +184,9 @@ def init_output_files(self):
             # Assemble virtual dataset
             layout = h5py.VirtualLayout(shape=(
                 self.nproj, self.nzi/2**self.args.binning, self.n), dtype=self.dtype)
-            os.system(f'mkdir -p {fnameout[:-3]}_parts')
+            if not os.path.exists(f'{fnameout[:-3]}_parts'):
+                os.makedirs(f'{fnameout[:-3]}_parts')
+
             for k in range(self.nzchunk):
                 filename = f"{fnameout[:-3]}_parts/p{k:04d}.h5"
                 vsource = h5py.VirtualSource(

diff --git a/tests/test_steps_try.py b/tests/test_steps_try.py
@@ -6,11 +6,11 @@
 
 prefix = 'tomocupy recon_steps --file-name data/test_data.h5 --rotation-axis 782.5 --nsino-per-chunk 4'
 cmd_dict = {
-    f'{prefix} --reconstruction-type try --lamino-angle 1 --reconstruction-algorithm linerec': 14.023,
-    f'{prefix} --reconstruction-type try_lamino --lamino-angle 1 --reconstruction-algorithm linerec': 37.060,
-    f'{prefix} --reconstruction-type try --rotate-proj-angle 1 --nsino [0,0.5]': 28.004,
-    f'{prefix} --reconstruction-type try --lamino-angle 1 --rotate-proj-angle 1 --nsino [0,0.5]': 26.180,    
-    f'{prefix} --reconstruction-type try --binning 1 --rotate-proj-angle 1 --nsino [0,0.5]': 11.103,    
+    f'{prefix} --center-search-width 10 --reconstruction-type try --lamino-angle 1 --reconstruction-algorithm linerec': 14.023,
+    f'{prefix} --center-search-width 10 --reconstruction-type try_lamino --lamino-angle 1 --reconstruction-algorithm linerec': 37.060,
+    f'{prefix} --center-search-width 10 --reconstruction-type try --rotate-proj-angle 1 --nsino [0,0.5]': 28.004,
+    f'{prefix} --center-search-width 10 --reconstruction-type try --lamino-angle 1 --rotate-proj-angle 1 --nsino [0,0.5]': 26.180,    
+    f'{prefix} --center-search-width 10 --reconstruction-type try --binning 1 --rotate-proj-angle 1 --nsino [0,0.5]': 11.103,    
 }
 
 

diff --git a/tests/test_try.py b/tests/test_try.py
@@ -6,15 +6,15 @@
 
 prefix = 'tomocupy recon --file-name data/test_data.h5 --reconstruction-type try --rotation-axis 782.5 --nsino-per-chunk 4'
 cmd_dict = {
-    f'{prefix} ': 13.98,
-    f'{prefix} --nsino [0,0.5] ': 28.36,
-    f'{prefix} --reconstruction-algorithm lprec ': 13.82,
-    f'{prefix} --reconstruction-algorithm linerec ': 14.00,
-    f'{prefix} --binning 1': 5.47,
-    f'{prefix} --nsino-per-chunk 2 --file-type double_fov': 7.67,
+    f'{prefix} --center-search-width 10 ': 13.98,
+    f'{prefix} --center-search-width 10 --nsino [0,0.5] ': 28.36,
+    f'{prefix} --center-search-width 10 --reconstruction-algorithm lprec ': 13.82,
+    f'{prefix} --center-search-width 10 --reconstruction-algorithm linerec ': 14.00,
+    f'{prefix} --center-search-width 10 --binning 1': 5.47,
+    f'{prefix} --center-search-width 10 --nsino-per-chunk 2 --file-type double_fov': 7.67,
     f'{prefix} --center-search-width 30 --center-search-step 2': 12.70,
-    f'{prefix} --dezinger 2': 13.98,
-    f'{prefix} --flat-linear True': 13.98,
+    f'{prefix} --center-search-width 10 --dezinger 2': 13.98,
+    f'{prefix} --center-search-width 10 --flat-linear True': 13.98,
 }