Fix

Author: NikoOinonen

Diff for: papers/ed-afm/figures/background_gradient.py

@@ -13,6 +13,7 @@
 from ppafm.ocl.AFMulator import AFMulator
 
 import mlspm.preprocessing as pp
+from mlspm.datasets import download_dataset
 from mlspm.models import EDAFMNet
 
 # # Set matplotlib font rendering to use LaTex
@@ -70,6 +71,9 @@ def apply_preprocessing_exp(X, real_dim):
     fontsize  = 8
     dpi       = 300
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+
     # Initialize OpenCL environment on GPU
     env = oclu.OCLEnvironment( i_platform = 0 )
     FFcl.init(env)

Diff for: papers/ed-afm/figures/bcb.py

@@ -15,6 +15,7 @@
 from scipy.ndimage import rotate, shift
 
 import mlspm.preprocessing as pp
+from mlspm.datasets import download_dataset
 from mlspm.models import EDAFMNet
 
 # # Set matplotlib font rendering to use LaTex
@@ -66,6 +67,9 @@ def apply_preprocessing_exp(X, real_dim):
     fontsize    = 8
     dpi         = 300
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+
     # Initialize OpenCL environment on GPU
     env = oclu.OCLEnvironment( i_platform = 0 )
     FFcl.init(env)

Diff for: papers/ed-afm/figures/esmap_sample.py

@@ -7,6 +7,7 @@
 import ppafm.ocl.field as FFcl
 import ppafm.ocl.oclUtils as oclu
 
+from mlspm.datasets import download_dataset
 from mlspm.utils import read_xyzs
 
 if __name__ == "__main__":
@@ -20,6 +21,9 @@
     zmin = -2.0
     Rpp = 1.0
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+
     # Initialize OpenCL environment on GPU
     env = oclu.OCLEnvironment(i_platform=0)
     FFcl.init(env)

Diff for: papers/ed-afm/figures/extra_electron.py

@@ -11,6 +11,7 @@
 from ppafm.ocl.AFMulator import AFMulator
 
 import mlspm.preprocessing as pp
+from mlspm.datasets import download_dataset
 
 # # Set matplotlib font rendering to use LaTex
 # plt.rcParams.update({
@@ -55,6 +56,9 @@ def apply_preprocessing(batch):
     fontsize    = 8
     dpi         = 300
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+
     # Initialize OpenCL environment on GPU
     env = oclu.OCLEnvironment( i_platform = 0 )
     FFcl.init(env)

Diff for: papers/ed-afm/figures/height_dependence.py

@@ -9,6 +9,7 @@
 from scipy.ndimage import rotate, shift
 
 import mlspm.preprocessing as pp
+from mlspm.datasets import download_dataset
 from mlspm.models import EDAFMNet
 
 # # Set matplotlib font rendering to use LaTex
@@ -56,6 +57,9 @@ def apply_preprocessing_ptcda(X, real_dim):
     fontsize    = 8
     dpi         = 300
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+
     # Load model
     model = EDAFMNet(device=device, pretrained_weights="base")
 

Diff for: papers/ed-afm/figures/ptcda.py

@@ -14,6 +14,7 @@
 from ppafm.ocl.AFMulator import AFMulator
 
 import mlspm.preprocessing as pp
+from mlspm.datasets import download_dataset
 from mlspm.models import EDAFMNet
 
 # # Set matplotlib font rendering to use LaTex
@@ -60,6 +61,9 @@ def apply_preprocessing_exp(X, real_dim):
     fontsize    = 8
     dpi         = 300
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+
     # Initialize OpenCL environment on GPU
     env = oclu.OCLEnvironment( i_platform = 0 )
     FFcl.init(env)

Diff for: papers/ed-afm/figures/ptcda_surface_sim.py

@@ -7,6 +7,7 @@
 from matplotlib import cm
 
 import mlspm.preprocessing as pp
+from mlspm.datasets import download_dataset
 from mlspm.models import EDAFMNet
 
 # # Set matplotlib font rendering to use LaTex
@@ -36,6 +37,9 @@ def apply_preprocessing(batch):
     fontsize    = 8
     dpi         = 300
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+
     # Load model
     model = EDAFMNet(device=device, pretrained_weights="base")
 

Diff for: papers/ed-afm/figures/sims.py

@@ -15,6 +15,7 @@
 from ppafm.ocl.AFMulator import AFMulator
 
 import mlspm.preprocessing as pp
+from mlspm.datasets import download_dataset
 from mlspm.models import EDAFMNet
 
 # # Set matplotlib font rendering to use LaTex
@@ -47,6 +48,9 @@ def apply_preprocessing(batch):
     fontsize    = 8
     dpi         = 300
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+
     # Initialize OpenCL environment on GPU
     env = oclu.OCLEnvironment(i_platform = 0)
     FFcl.init(env)

Diff for: papers/ed-afm/figures/sims_Cl.py

@@ -15,6 +15,7 @@
 from ppafm.ocl.AFMulator import AFMulator
 
 import mlspm.preprocessing as pp
+from mlspm.datasets import download_dataset
 from mlspm.models import EDAFMNet
 
 # # Set matplotlib font rendering to use LaTex
@@ -57,6 +58,9 @@ def apply_preprocessing(batch):
     fontsize    = 8
     dpi         = 300
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+
     # Initialize OpenCL environment on GPU
     env = oclu.OCLEnvironment( i_platform = 0 )
     FFcl.init(env)

Diff for: papers/ed-afm/figures/sims_hartree.py

@@ -8,6 +8,7 @@
 from matplotlib import cm
 
 import mlspm.preprocessing as pp
+from mlspm.datasets import download_dataset
 from mlspm.models import EDAFMNet
 
 # # Set matplotlib font rendering to use LaTex
@@ -40,6 +41,9 @@ def apply_preprocessing(batch):
 
     molecules = [data_dir / m for m in molecules]
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+    
     # Load model
     model = EDAFMNet(device=device, pretrained_weights="base")
 

Diff for: papers/ed-afm/figures/single_tip.py

@@ -13,6 +13,7 @@
 from ppafm.ocl.AFMulator import AFMulator
 
 import mlspm.preprocessing as pp
+from mlspm.datasets import download_dataset
 from mlspm.models import EDAFMNet
 
 # # Set matplotlib font rendering to use LaTex
@@ -57,6 +58,9 @@ def apply_preprocessing_ptcda(X, real_dim):
     fontsize    = 8
     dpi         = 300
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+
     # Initialize OpenCL environment on GPU
     env = oclu.OCLEnvironment( i_platform = 0 )
     FFcl.init(env)

Diff for: papers/ed-afm/figures/stats.py

@@ -1,5 +1,4 @@
 
-import os
 from pathlib import Path
 import tarfile
 import numpy as np

Diff for: papers/ed-afm/figures/surface_sims_bcb_water.py

@@ -9,6 +9,7 @@
 from matplotlib import cm
 
 import mlspm.preprocessing as pp
+from mlspm.datasets import download_dataset
 from mlspm.models import EDAFMNet
 
 # # Set matplotlib font rendering to use LaTex
@@ -41,6 +42,9 @@ def apply_preprocessing(batch):
 
     molecules = [data_dir / m for m in molecules]
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+
     # Load model
     model = EDAFMNet(device=device, pretrained_weights="base")
 

Diff for: papers/ed-afm/figures/water.py

@@ -14,6 +14,7 @@
 from ppafm.ocl.AFMulator import AFMulator
 
 import mlspm.preprocessing as pp
+from mlspm.datasets import download_dataset
 from mlspm.models import EDAFMNet
 
 # # Set matplotlib font rendering to use LaTex
@@ -78,6 +79,9 @@ def apply_preprocessing_exp(X, real_dim):
     fontsize    = 8
     dpi         = 300
 
+    # Download data if not already there
+    download_dataset("ED-AFM-data", data_dir)
+
     # Initialize OpenCL environment on GPU
     env = oclu.OCLEnvironment( i_platform = 0 )
     FFcl.init(env)