integrate_module 0.99.1__tar.gz → 0.99.3__tar.gz

{integrate_module-0.99.1/integrate_module.egg-info → integrate_module-0.99.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: integrate_module
-Version: 0.99.1
+Version: 0.99.3
 Summary: Localized probabilistic data integration
 Author-email: Thomas Mejer Hansen <tmeha@geo.au.dk>
 License: MIT
@@ -30,6 +30,7 @@ Requires-Dist: pyvista
 Requires-Dist: litellm
 Requires-Dist: streamlit
 Requires-Dist: libaarhusxyz
+Requires-Dist: jax
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: black; extra == "dev"

{integrate_module-0.99.1 → integrate_module-0.99.3}/integrate/__init__.py

@@ -18,8 +18,9 @@ from integrate.integrate_rejection import create_shared_memory
 from integrate.integrate_rejection import compute_hypothesis_probability
 
 # Import other functions from main module
-from integrate.integrate import integrate_update_prior_attributes   
+from integrate.integrate import integrate_update_prior_attributes
 from integrate.integrate import integrate_posterior_stats
+from integrate.integrate import prior_set
 from integrate.integrate import logl_T_est
 from integrate.integrate import lu_post_sample_logl
 from integrate.integrate import prior_data

{integrate_module-0.99.1 → integrate_module-0.99.3}/integrate/integrate.py

@@ -287,6 +287,131 @@ def integrate_update_prior_attributes(f_prior_h5, **kwargs):
 
 
 
+def prior_set(f_prior_h5, im=1, **kwargs):
+    """
+    Update attributes of a model parameter in a prior HDF5 file.
+
+    Parameters
+    ----------
+    f_prior_h5 : str
+        Path to the prior HDF5 file to update.
+    im : int
+        Model parameter index (e.g., 1 for /M1, 2 for /M2, default is 1).
+    name : str, optional
+        Display name of the model parameter (e.g., 'Resistivity', 'Lithology').
+    class_name : list of str, optional
+        Class names for discrete parameters. If fewer names than existing classes
+        are given, only the first N entries are updated and the rest are kept.
+    color : list of str or RGBA tuples, optional
+        Per-class colors (e.g., ['blue', 'red']). Converted to RGBA and stored
+        as the ``cmap`` attribute. If fewer colors than existing classes are given,
+        only the first N entries are updated and the rest are kept.
+    class_id : array-like, optional
+        Class ID values for discrete parameters.
+    clim : list of float, optional
+        Color scale limits [min, max].
+    is_discrete : int or bool, optional
+        Whether the parameter is discrete (1) or continuous (0).
+    cmap : str or array-like, optional
+        Colormap. Either a matplotlib colormap name (colors are sampled to match
+        the number of classes) or an RGBA array of shape (4, N).
+
+    Examples
+    --------
+    >>> ig.prior_set('PRIOR.h5', im=1, name='Resistivity', clim=[1, 2600])
+    >>> ig.prior_set('PRIOR.h5', im=2, class_name=['Sand', 'Clay', 'Gravel'])
+    >>> ig.prior_set('PRIOR.h5', im=2, class_name=['inside valley', 'outside valley'],
+    ...              color=['blue', 'red'])
+    """
+    import matplotlib.colors as mcolors
+    import matplotlib
+
+    def _set_attr(ds, key, value):
+        # Delete first to avoid h5py silently failing on dtype/shape changes
+        if key in ds.attrs:
+            del ds.attrs[key]
+        ds.attrs[key] = value
+
+    def _decode(v):
+        return v.decode('utf-8') if isinstance(v, bytes) else str(v)
+
+    Mstr = 'M%d' % im
+
+    if not os.path.exists(f_prior_h5):
+        print('prior_set: File %s does not exist (will not create)' % f_prior_h5)
+        return
+
+    with h5py.File(f_prior_h5, 'a') as f:
+        if Mstr not in f:
+            print('prior_set: %s not found in %s' % (Mstr, f_prior_h5))
+            return
+
+        ds = f[Mstr]
+
+        if 'name' in kwargs:
+            _set_attr(ds, 'name', str(kwargs['name']))
+            print('prior_set: %s/name = %r' % (Mstr, kwargs['name']))
+
+        if 'class_name' in kwargs:
+            new_names = [str(n) for n in kwargs['class_name']]
+            if 'class_name' in ds.attrs:
+                existing = [_decode(n) for n in ds.attrs['class_name']]
+                for i, n in enumerate(new_names):
+                    if i < len(existing):
+                        existing[i] = n
+                    else:
+                        existing.append(n)
+                final = existing
+            else:
+                final = new_names
+            _set_attr(ds, 'class_name', [str(n) for n in final])
+            print('prior_set: %s/class_name = %s' % (Mstr, list(ds.attrs['class_name'])))
+
+        if 'color' in kwargs:
+            new_colors = [np.array(mcolors.to_rgba(c)) for c in kwargs['color']]
+            n_new = len(new_colors)
+            if 'cmap' in ds.attrs:
+                existing_rgba = ds.attrs['cmap'].T  # (N, 4)
+                existing_list = [existing_rgba[i] for i in range(len(existing_rgba))]
+                for i, c in enumerate(new_colors):
+                    if i < len(existing_list):
+                        existing_list[i] = c
+                    else:
+                        existing_list.append(c)
+                rgba = np.array(existing_list)
+            else:
+                rgba = np.array(new_colors)
+            _set_attr(ds, 'cmap', rgba.T)  # stored as (4, N)
+            print('prior_set: %s/cmap updated from color list (%d colors)' % (Mstr, n_new))
+
+        if 'class_id' in kwargs:
+            _set_attr(ds, 'class_id', np.array(kwargs['class_id']))
+            print('prior_set: %s/class_id = %s' % (Mstr, ds.attrs['class_id']))
+
+        if 'clim' in kwargs:
+            _set_attr(ds, 'clim', np.array(kwargs['clim'], dtype=float))
+            print('prior_set: %s/clim = %s' % (Mstr, ds.attrs['clim']))
+
+        if 'is_discrete' in kwargs:
+            _set_attr(ds, 'is_discrete', int(kwargs['is_discrete']))
+            print('prior_set: %s/is_discrete = %d' % (Mstr, ds.attrs['is_discrete']))
+
+        if 'cmap' in kwargs:
+            cmap_val = kwargs['cmap']
+            if isinstance(cmap_val, str):
+                if 'class_id' in ds.attrs:
+                    n_colors = len(ds.attrs['class_id'])
+                elif 'class_name' in ds.attrs:
+                    n_colors = len(ds.attrs['class_name'])
+                else:
+                    n_colors = 10
+                rgba = matplotlib.colormaps[cmap_val](np.linspace(0, 1, n_colors))
+            else:
+                rgba = np.array(cmap_val)
+            _set_attr(ds, 'cmap', rgba.T)  # stored as (4, N)
+            print('prior_set: %s/cmap updated' % Mstr)
+
+
 def integrate_posterior_stats(f_post_h5='POST.h5', ip_range=None, **kwargs):
     """
     Compute posterior statistics for all model parameters in a POST HDF5 file.
@@ -3306,37 +3431,41 @@ def timing_compute(N_arr=[], Nproc_arr=[], backend='numpy', NcpuForward=0):
     return file_out
 
 
-def timing_plot(f_timing=''):
+def timing_plot(f_timing='', fontsize=16):
     """
     Generate comprehensive timing analysis plots from benchmark results.
-    
+
     This function creates multiple plots analyzing the performance characteristics
     of the INTEGRATE workflow across different dataset sizes and processor counts.
-    
+
     Parameters
     ----------
     f_timing : str
         Path to NPZ file containing timing benchmark results from timing_compute().
-        
+    fontsize : int, optional
+        Base font size for all plot text (labels, titles, ticks, legends).
+        Default is 16.
+
     Returns
     -------
     None
         Saves multiple PNG files with timing analysis plots.
-        
+
     Notes
     -----
     Generated plots include:
     - Total execution time vs processors and dataset size
-    - Forward modeling performance and speedup analysis  
+    - Forward modeling performance and speedup analysis
     - Rejection sampling performance and scaling
     - Posterior statistics computation performance
     - Cumulative time breakdowns for different processor counts
     - Comparisons with traditional least squares and MCMC methods
-    
+
     The function handles missing data gracefully and includes reference lines
     for linear scaling to assess parallel efficiency.
     """
     import numpy as np
+    import matplotlib as mpl
     import matplotlib.pyplot as plt
 
     def safe_show():
@@ -3351,6 +3480,15 @@ def timing_plot(f_timing=''):
     else:
         print('Plotting timing results from %s' % f_timing)
 
+    mpl.rcParams.update({
+        'font.size': fontsize,
+        'axes.labelsize': fontsize,
+        'axes.titlesize': fontsize + 2,
+        'xtick.labelsize': fontsize - 2,
+        'ytick.labelsize': fontsize - 2,
+        'legend.fontsize': fontsize - 2,
+    })
+
     # file_out is f_timing, without file extension
     file_out = f_timing.split('.')[0]
     

{integrate_module-0.99.1 → integrate_module-0.99.3}/integrate/integrate_io.py

@@ -2967,6 +2967,10 @@ def get_case_data(case='DAUGAARD', loadAll=False, loadType='', filelist=None, **
         print("filelist to download:")
         print(filelist)
 
+    # Direct-download endpoint for the shared data. Use ERDA's 'share_redirect'
+    # form (serves raw file bytes, returns proper 404s), NOT the 'sharelink'
+    # browse link, which returns an HTML directory page with status 200 for any
+    # path and would be saved as a corrupt file.
     urlErda = 'https://anon.erda.au.dk/share_redirect/dxOLKDtoul'
     urlErdaCase = '%s/%s' % (urlErda,case)
     from tqdm import tqdm
@@ -2976,7 +2980,22 @@ def get_case_data(case='DAUGAARD', loadAll=False, loadType='', filelist=None, **
     if showInfo>-1:
         print('--> Got data for case: %s' % case)
 
-    return [f.replace('\\', '/').split('/')[-1] for f in filelist]
+    # Return the local filename for each requested file, but only if it was
+    # actually obtained (downloaded or already present locally). download_file
+    # saves to download_dir='.' using the basename, so we check for that here.
+    # Files that could not be obtained (e.g. missing on the remote server)
+    # return an empty string, so callers can test `if len(name) == 0`.
+    result = []
+    for f in filelist:
+        basename = f.replace('\\', '/').split('/')[-1]
+        if os.path.exists(basename):
+            result.append(basename)
+        else:
+            if showInfo>-1:
+                print('File %s was not obtained (missing locally and on remote); returning empty string.' % basename)
+            result.append('')
+
+    return result