From bb7bcfd3fb79bf737f0e861fdaef282960d70d46 Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Fri, 9 May 2025 08:34:01 +0200
Subject: [PATCH 01/16] initial commit

---
 src/easyreflectometry/model/__init__.py       |  2 +
 src/easyreflectometry/model/model.py          |  1 +
 .../model/resolution_functions.py             | 49 +++++++++++++++++++
 src/easyreflectometry/project.py              | 15 ++++--
 tests/model/test_resolution_functions.py      | 35 +++++++++++++
 tests/test_project.py                         |  3 +-
 6 files changed, 100 insertions(+), 5 deletions(-)

diff --git a/src/easyreflectometry/model/__init__.py b/src/easyreflectometry/model/__init__.py
index baa1aec4..40cef321 100644
--- a/src/easyreflectometry/model/__init__.py
+++ b/src/easyreflectometry/model/__init__.py
@@ -3,10 +3,12 @@
 from .resolution_functions import LinearSpline
 from .resolution_functions import PercentageFwhm
 from .resolution_functions import ResolutionFunction
+from .resolution_functions import Pointwise
 
 __all__ = (
     "LinearSpline",
     "PercentageFwhm",
+    "Pointwise",
     "ResolutionFunction",
     "Model",
     "ModelCollection",
diff --git a/src/easyreflectometry/model/model.py b/src/easyreflectometry/model/model.py
index 969c955a..a06bfc00 100644
--- a/src/easyreflectometry/model/model.py
+++ b/src/easyreflectometry/model/model.py
@@ -19,6 +19,7 @@
 
 from .resolution_functions import PercentageFwhm
 from .resolution_functions import ResolutionFunction
+from .resolution_functions import Pointwise
 
 DEFAULTS = {
     'scale': {
diff --git a/src/easyreflectometry/model/resolution_functions.py b/src/easyreflectometry/model/resolution_functions.py
index 3a352fc5..6dd3ad7e 100644
--- a/src/easyreflectometry/model/resolution_functions.py
+++ b/src/easyreflectometry/model/resolution_functions.py
@@ -30,6 +30,8 @@ def from_dict(cls, data: dict) -> ResolutionFunction:
             return PercentageFwhm(data['constant'])
         if data['smearing'] == 'LinearSpline':
             return LinearSpline(data['q_data_points'], data['fwhm_values'])
+        if data['smearing'] == 'Pointwise':
+            return Pointwise(data['q_data_points'])
         raise ValueError('Unknown resolution function type')
 
 
@@ -60,3 +62,50 @@ def as_dict(
         self, skip: Optional[List[str]] = None
     ) -> dict[str, str]:  # skip is kept for consistency of the as_dict signature
         return {'smearing': 'LinearSpline', 'q_data_points': list(self.q_data_points), 'fwhm_values': list(self.fwhm_values)}
+
+# add pointwise smearing funtion
+class Pointwise(ResolutionFunction):
+    def __init__(self, q_data_points: np.array):
+        self.q_data_points = q_data_points
+
+    def smearing(self, q: Union[np.array, float] = 0.0) -> np.array:
+
+        Qz= self.q_data_points[0]
+        R= self.q_data_points[1]
+        sR= self.q_data_points[2]
+        sQz= self.q_data_points[3]
+        smeared = self.apply_smooth_smearing(Qz, R, sR, sQz)
+        return smeared
+
+    def as_dict(
+        self, skip: Optional[List[str]] = None
+    ) -> dict[str, str]:  # skip is kept for consistency of the as_dict signature
+        return {'smearing': 'Pointwise', 'q_data_points': list(self.q_data_points)}
+
+    def gaussian_kernel(self, x, sigma):
+        """Simple Gaussian kernel function"""
+        return np.exp(-x**2/(2*sigma**2))
+
+    def apply_smooth_smearing(self, Qz, R, sR, sQz, n_sigma=3):
+        """
+        Apply smooth resolution smearing using convolution with Gaussian kernel.
+        """
+        R_smeared = np.zeros_like(R)
+        if not isinstance(Qz, np.ndarray):
+            Qz = np.array(Qz)
+        if not isinstance(R, np.ndarray):
+            R = np.array(R)
+        for i, (q, r, sr, sq) in enumerate(zip(Qz, R, sR, sQz)):
+            weights = self.gaussian_kernel(Qz - q, sq)
+            mask = np.abs(Qz - q) <= n_sigma * sq
+            weights[~mask] = 0
+
+            if np.sum(weights) > 0:
+                weights = weights / np.sum(weights)
+
+            R_smeared[i] = np.sum(R * weights)
+            # Potentially add the pointwise error from sR
+            # This can also be used as error bands
+            # R_smeared[i] += np.random.normal(0, sr * weights[i])
+
+        return R_smeared
\ No newline at end of file
diff --git a/src/easyreflectometry/project.py b/src/easyreflectometry/project.py
index de769ab8..93a3f74f 100644
--- a/src/easyreflectometry/project.py
+++ b/src/easyreflectometry/project.py
@@ -22,6 +22,7 @@
 from easyreflectometry.model import Model
 from easyreflectometry.model import ModelCollection
 from easyreflectometry.model import PercentageFwhm
+from easyreflectometry.model import Pointwise
 from easyreflectometry.sample import Layer
 from easyreflectometry.sample import Material
 from easyreflectometry.sample import MaterialCollection
@@ -249,10 +250,16 @@ def load_experiment_for_model_at_index(self, path: Union[Path, str], index: Opti
 
         # Set the resolution function if variance data is present
         if sum(self._experiments[index].ye) != 0:
-            resolution_function = LinearSpline(
-                q_data_points=self._experiments[index].y,
-                fwhm_values=np.sqrt(self._experiments[index].ye),
-            )
+            q = self._experiments[index].x
+            reflectivity = self._experiments[index].y
+            reflectivity_error = self._experiments[index].ye
+            q_error = self._experiments[index].xe
+            resolution_function = Pointwise(
+                q_data_points=[q, reflectivity, reflectivity_error, q_error])
+            # resolution_function = LinearSpline(
+            #     q_data_points=self._experiments[index].y,
+            #     fwhm_values=np.sqrt(self._experiments[index].ye),
+            # )
             self._models[index].resolution_function = resolution_function
 
     def sld_data_for_model_at_index(self, index: int = 0) -> DataSet1D:
diff --git a/tests/model/test_resolution_functions.py b/tests/model/test_resolution_functions.py
index f2963c48..bcf4e0ac 100644
--- a/tests/model/test_resolution_functions.py
+++ b/tests/model/test_resolution_functions.py
@@ -6,6 +6,7 @@
 from easyreflectometry.model.resolution_functions import LinearSpline
 from easyreflectometry.model.resolution_functions import PercentageFwhm
 from easyreflectometry.model.resolution_functions import ResolutionFunction
+from easyreflectometry.model.resolution_functions import Pointwise
 
 
 class TestPercentageFwhm(unittest.TestCase):
@@ -75,3 +76,37 @@ def test_dict_round_trip(self):
 
         # Expect
         assert all(resolution_function.smearing([0, 2.5]) == expected_resolution_function.smearing([0, 2.5]))
+
+class TestPointwise(unittest.TestCase):
+
+    data_points = []
+    data_points.append([0.1, 0.2, 0.3, 0.4, 0.5]) # Qz
+    data_points.append([1.1, 2.2, 3.3, 4.4, 5.5]) # R
+    data_points.append([0.01, 0.02, 0.01, 0.05, 0.08]) # sR
+    data_points.append([0.03, 0.04, 0.05, 0.06, 0.07]) # sQz
+    def test_constructor(self):
+
+        # When
+        resolution_function = Pointwise(q_data_points=self.data_points)
+
+        # Then Expect
+        assert np.allclose(np.array(resolution_function.smearing()), np.array([1.1, 2.2, 3.3, 4.4, 5.18516692]))
+
+
+    def test_as_dict(self):
+        # When
+        resolution_function = Pointwise(q_data_points=self.data_points)
+
+        # Then Expect
+        resolution_function.as_dict() == {'smearing': 'Pointwise', 'q_data_points': [0, 10]}
+
+    def test_dict_round_trip(self):
+        # When
+        expected_resolution_function = Pointwise(q_data_points=self.data_points)
+        res_dict = expected_resolution_function.as_dict()
+
+        # Then
+        resolution_function = ResolutionFunction.from_dict(res_dict)
+
+        # Expect
+        assert all(resolution_function.smearing() == expected_resolution_function.smearing())
diff --git a/tests/test_project.py b/tests/test_project.py
index 523138c3..f1ded171 100644
--- a/tests/test_project.py
+++ b/tests/test_project.py
@@ -16,6 +16,7 @@
 from easyreflectometry.model import Model
 from easyreflectometry.model import ModelCollection
 from easyreflectometry.model import PercentageFwhm
+from easyreflectometry.model import Pointwise
 from easyreflectometry.project import Project
 from easyreflectometry.sample import Material
 from easyreflectometry.sample import MaterialCollection
@@ -561,7 +562,7 @@ def test_load_experiment(self):
         assert isinstance(project.experiments[5], DataSet1D)
         assert project.experiments[5].name == 'Experiment for Model 5'
         assert project.experiments[5].model == model_5
-        assert isinstance(project.models[5].resolution_function, LinearSpline)
+        assert isinstance(project.models[5].resolution_function, Pointwise)
         assert isinstance(project.models[4].resolution_function, PercentageFwhm)
 
     def test_experimental_data_at_index(self):

From c8f70d152b56982723057aa217b3d45a68461be3 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Fri, 9 May 2025 09:47:23 +0200
Subject: [PATCH 02/16] ruff

---
 src/easyreflectometry/model/__init__.py  | 2 +-
 src/easyreflectometry/model/model.py     | 1 -
 src/easyreflectometry/project.py         | 1 -
 tests/model/test_resolution_functions.py | 2 +-
 tests/test_project.py                    | 1 -
 5 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/easyreflectometry/model/__init__.py b/src/easyreflectometry/model/__init__.py
index 40cef321..b12b504e 100644
--- a/src/easyreflectometry/model/__init__.py
+++ b/src/easyreflectometry/model/__init__.py
@@ -2,8 +2,8 @@
 from .model_collection import ModelCollection
 from .resolution_functions import LinearSpline
 from .resolution_functions import PercentageFwhm
-from .resolution_functions import ResolutionFunction
 from .resolution_functions import Pointwise
+from .resolution_functions import ResolutionFunction
 
 __all__ = (
     "LinearSpline",
diff --git a/src/easyreflectometry/model/model.py b/src/easyreflectometry/model/model.py
index a06bfc00..969c955a 100644
--- a/src/easyreflectometry/model/model.py
+++ b/src/easyreflectometry/model/model.py
@@ -19,7 +19,6 @@
 
 from .resolution_functions import PercentageFwhm
 from .resolution_functions import ResolutionFunction
-from .resolution_functions import Pointwise
 
 DEFAULTS = {
     'scale': {
diff --git a/src/easyreflectometry/project.py b/src/easyreflectometry/project.py
index 93a3f74f..787877fa 100644
--- a/src/easyreflectometry/project.py
+++ b/src/easyreflectometry/project.py
@@ -18,7 +18,6 @@
 from easyreflectometry.data import DataSet1D
 from easyreflectometry.data import load_as_dataset
 from easyreflectometry.fitting import MultiFitter
-from easyreflectometry.model import LinearSpline
 from easyreflectometry.model import Model
 from easyreflectometry.model import ModelCollection
 from easyreflectometry.model import PercentageFwhm
diff --git a/tests/model/test_resolution_functions.py b/tests/model/test_resolution_functions.py
index bcf4e0ac..0a609826 100644
--- a/tests/model/test_resolution_functions.py
+++ b/tests/model/test_resolution_functions.py
@@ -5,8 +5,8 @@
 from easyreflectometry.model.resolution_functions import DEFAULT_RESOLUTION_FWHM_PERCENTAGE
 from easyreflectometry.model.resolution_functions import LinearSpline
 from easyreflectometry.model.resolution_functions import PercentageFwhm
-from easyreflectometry.model.resolution_functions import ResolutionFunction
 from easyreflectometry.model.resolution_functions import Pointwise
+from easyreflectometry.model.resolution_functions import ResolutionFunction
 
 
 class TestPercentageFwhm(unittest.TestCase):
diff --git a/tests/test_project.py b/tests/test_project.py
index f1ded171..bfa6c233 100644
--- a/tests/test_project.py
+++ b/tests/test_project.py
@@ -12,7 +12,6 @@
 import easyreflectometry
 from easyreflectometry.data import DataSet1D
 from easyreflectometry.fitting import MultiFitter
-from easyreflectometry.model import LinearSpline
 from easyreflectometry.model import Model
 from easyreflectometry.model import ModelCollection
 from easyreflectometry.model import PercentageFwhm

From ddc90a6a7c0e50822117558cdaf470d4704c0356 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Fri, 9 May 2025 10:48:56 +0200
Subject: [PATCH 03/16] fixed unit tests

---
 src/easyreflectometry/project.py | 22 +++++++++++-----------
 tests/test_project.py            |  4 ++--
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/easyreflectometry/project.py b/src/easyreflectometry/project.py
index 787877fa..6ba43b28 100644
--- a/src/easyreflectometry/project.py
+++ b/src/easyreflectometry/project.py
@@ -18,10 +18,10 @@
 from easyreflectometry.data import DataSet1D
 from easyreflectometry.data import load_as_dataset
 from easyreflectometry.fitting import MultiFitter
+from easyreflectometry.model import LinearSpline
 from easyreflectometry.model import Model
 from easyreflectometry.model import ModelCollection
 from easyreflectometry.model import PercentageFwhm
-from easyreflectometry.model import Pointwise
 from easyreflectometry.sample import Layer
 from easyreflectometry.sample import Material
 from easyreflectometry.sample import MaterialCollection
@@ -249,16 +249,16 @@ def load_experiment_for_model_at_index(self, path: Union[Path, str], index: Opti
 
         # Set the resolution function if variance data is present
         if sum(self._experiments[index].ye) != 0:
-            q = self._experiments[index].x
-            reflectivity = self._experiments[index].y
-            reflectivity_error = self._experiments[index].ye
-            q_error = self._experiments[index].xe
-            resolution_function = Pointwise(
-                q_data_points=[q, reflectivity, reflectivity_error, q_error])
-            # resolution_function = LinearSpline(
-            #     q_data_points=self._experiments[index].y,
-            #     fwhm_values=np.sqrt(self._experiments[index].ye),
-            # )
+            # q = self._experiments[index].x
+            # reflectivity = self._experiments[index].y
+            # reflectivity_error = self._experiments[index].ye
+            # q_error = self._experiments[index].xe
+            # resolution_function = Pointwise(
+            #     q_data_points=[q, reflectivity, reflectivity_error, q_error])
+            resolution_function = LinearSpline(
+                q_data_points=self._experiments[index].y,
+                fwhm_values=np.sqrt(self._experiments[index].ye),
+            )
             self._models[index].resolution_function = resolution_function
 
     def sld_data_for_model_at_index(self, index: int = 0) -> DataSet1D:
diff --git a/tests/test_project.py b/tests/test_project.py
index bfa6c233..523138c3 100644
--- a/tests/test_project.py
+++ b/tests/test_project.py
@@ -12,10 +12,10 @@
 import easyreflectometry
 from easyreflectometry.data import DataSet1D
 from easyreflectometry.fitting import MultiFitter
+from easyreflectometry.model import LinearSpline
 from easyreflectometry.model import Model
 from easyreflectometry.model import ModelCollection
 from easyreflectometry.model import PercentageFwhm
-from easyreflectometry.model import Pointwise
 from easyreflectometry.project import Project
 from easyreflectometry.sample import Material
 from easyreflectometry.sample import MaterialCollection
@@ -561,7 +561,7 @@ def test_load_experiment(self):
         assert isinstance(project.experiments[5], DataSet1D)
         assert project.experiments[5].name == 'Experiment for Model 5'
         assert project.experiments[5].model == model_5
-        assert isinstance(project.models[5].resolution_function, Pointwise)
+        assert isinstance(project.models[5].resolution_function, LinearSpline)
         assert isinstance(project.models[4].resolution_function, PercentageFwhm)
 
     def test_experimental_data_at_index(self):

From ade4d9a017d2d315a628ce4c0d4a3c6067d68d66 Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Fri, 23 May 2025 13:06:47 +0200
Subject: [PATCH 04/16] updated smearing

---
 .../model/resolution_functions.py             | 68 ++++++++++++-------
 1 file changed, 43 insertions(+), 25 deletions(-)

diff --git a/src/easyreflectometry/model/resolution_functions.py b/src/easyreflectometry/model/resolution_functions.py
index 6dd3ad7e..7fd7f28c 100644
--- a/src/easyreflectometry/model/resolution_functions.py
+++ b/src/easyreflectometry/model/resolution_functions.py
@@ -11,6 +11,7 @@
 from typing import List
 from typing import Optional
 from typing import Union
+import scipp as sc
 
 import numpy as np
 
@@ -65,16 +66,21 @@ def as_dict(
 
 # add pointwise smearing funtion
 class Pointwise(ResolutionFunction):
-    def __init__(self, q_data_points: np.array):
+    def __init__(self, q_data_points: sc.DataGroup):
         self.q_data_points = q_data_points
+        self.q = None
 
     def smearing(self, q: Union[np.array, float] = 0.0) -> np.array:
 
-        Qz= self.q_data_points[0]
-        R= self.q_data_points[1]
-        sR= self.q_data_points[2]
-        sQz= self.q_data_points[3]
-        smeared = self.apply_smooth_smearing(Qz, R, sR, sQz)
+        Qz = self.q_data_points[0]
+        R = self.q_data_points[1]
+        sQz = self.q_data_points[2]
+        self.q = q
+        sQzs = np.sqrt(sQz)
+        if not isinstance(q, np.ndarray):
+            q = np.ndarray(q)
+
+        smeared = self.apply_smooth_smearing(Qz, R, sQzs)
         return smeared
 
     def as_dict(
@@ -82,30 +88,42 @@ def as_dict(
     ) -> dict[str, str]:  # skip is kept for consistency of the as_dict signature
         return {'smearing': 'Pointwise', 'q_data_points': list(self.q_data_points)}
 
-    def gaussian_kernel(self, x, sigma):
-        """Simple Gaussian kernel function"""
-        return np.exp(-x**2/(2*sigma**2))
+    def gaussian_smearing(self, qt, Qz, R, sQz):
+        weights = np.exp(-0.5 * ((qt - Qz) / sQz) ** 2)
+        if np.sum(weights) == 0 or not np.isfinite(np.sum(weights)):
+            return R
+        weights /= (sQz * np.sqrt(2 * np.pi))
+        return np.sum(R * weights) / np.sum(weights)
+
 
-    def apply_smooth_smearing(self, Qz, R, sR, sQz, n_sigma=3):
+    def apply_smooth_smearing(self, Qz, R, sQzs):
         """
         Apply smooth resolution smearing using convolution with Gaussian kernel.
         """
-        R_smeared = np.zeros_like(R)
+        if self.q is None:
+            R_smeared = np.zeros_like(Qz)
+        else:
+            R_smeared = np.zeros_like(self.q)
         if not isinstance(Qz, np.ndarray):
             Qz = np.array(Qz)
         if not isinstance(R, np.ndarray):
             R = np.array(R)
-        for i, (q, r, sr, sq) in enumerate(zip(Qz, R, sR, sQz)):
-            weights = self.gaussian_kernel(Qz - q, sq)
-            mask = np.abs(Qz - q) <= n_sigma * sq
-            weights[~mask] = 0
-
-            if np.sum(weights) > 0:
-                weights = weights / np.sum(weights)
-
-            R_smeared[i] = np.sum(R * weights)
-            # Potentially add the pointwise error from sR
-            # This can also be used as error bands
-            # R_smeared[i] += np.random.normal(0, sr * weights[i])
-
-        return R_smeared
\ No newline at end of file
+        R_smeared = np.zeros_like(self.q)
+
+        for i, qt in enumerate(self.q):
+            R_smeared[i] = self.gaussian_smearing(qt, Qz, R, sQzs)
+
+        # TEST LOCALLY
+        # import matplotlib.pyplot as plt
+        # plt.figure(figsize=(10, 6))
+        # plt.plot(Qz, R, label='Original R', marker='o', linestyle='none')
+        # plt.plot(self.q, R_smeared, label='Smeared R', linestyle='-')
+        # plt.yscale('log')
+        # plt.xlabel('Qz (1/angstrom)')
+        # plt.ylabel('R')
+        # plt.legend()
+        # plt.title('Original and Smeared R vs Qz (log scale)')
+        # plt.grid(True)
+        # plt.show()
+
+        return R_smeared

From e93b0f3b1c432c21802b6d9d9646bd5ea627aed9 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Mon, 26 May 2025 10:40:06 +0200
Subject: [PATCH 05/16] fix unit tests

---
 src/easyreflectometry/model/resolution_functions.py | 11 ++++++-----
 src/easyreflectometry/project.py                    |  2 +-
 tests/model/test_resolution_functions.py            |  4 +---
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/src/easyreflectometry/model/resolution_functions.py b/src/easyreflectometry/model/resolution_functions.py
index 7fd7f28c..7fdf5e87 100644
--- a/src/easyreflectometry/model/resolution_functions.py
+++ b/src/easyreflectometry/model/resolution_functions.py
@@ -11,7 +11,6 @@
 from typing import List
 from typing import Optional
 from typing import Union
-import scipp as sc
 
 import numpy as np
 
@@ -66,19 +65,21 @@ def as_dict(
 
 # add pointwise smearing funtion
 class Pointwise(ResolutionFunction):
-    def __init__(self, q_data_points: sc.DataGroup):
+    def __init__(self, q_data_points: list[np.ndarray]):
         self.q_data_points = q_data_points
         self.q = None
 
-    def smearing(self, q: Union[np.array, float] = 0.0) -> np.array:
+    def smearing(self, q: Union[np.ndarray, float] = None) -> np.ndarray:
 
         Qz = self.q_data_points[0]
         R = self.q_data_points[1]
         sQz = self.q_data_points[2]
+        if q is None:
+            q = self.q_data_points[0]
         self.q = q
         sQzs = np.sqrt(sQz)
-        if not isinstance(q, np.ndarray):
-            q = np.ndarray(q)
+        if isinstance(Qz, float):
+            Qz = np.array(Qz)
 
         smeared = self.apply_smooth_smearing(Qz, R, sQzs)
         return smeared
diff --git a/src/easyreflectometry/project.py b/src/easyreflectometry/project.py
index 6ba43b28..e183ea40 100644
--- a/src/easyreflectometry/project.py
+++ b/src/easyreflectometry/project.py
@@ -254,7 +254,7 @@ def load_experiment_for_model_at_index(self, path: Union[Path, str], index: Opti
             # reflectivity_error = self._experiments[index].ye
             # q_error = self._experiments[index].xe
             # resolution_function = Pointwise(
-            #     q_data_points=[q, reflectivity, reflectivity_error, q_error])
+            #     q_data_points=[q, reflectivity, q_error])
             resolution_function = LinearSpline(
                 q_data_points=self._experiments[index].y,
                 fwhm_values=np.sqrt(self._experiments[index].ye),
diff --git a/tests/model/test_resolution_functions.py b/tests/model/test_resolution_functions.py
index 0a609826..ab6e0e4e 100644
--- a/tests/model/test_resolution_functions.py
+++ b/tests/model/test_resolution_functions.py
@@ -82,7 +82,6 @@ class TestPointwise(unittest.TestCase):
     data_points = []
     data_points.append([0.1, 0.2, 0.3, 0.4, 0.5]) # Qz
     data_points.append([1.1, 2.2, 3.3, 4.4, 5.5]) # R
-    data_points.append([0.01, 0.02, 0.01, 0.05, 0.08]) # sR
     data_points.append([0.03, 0.04, 0.05, 0.06, 0.07]) # sQz
     def test_constructor(self):
 
@@ -90,8 +89,7 @@ def test_constructor(self):
         resolution_function = Pointwise(q_data_points=self.data_points)
 
         # Then Expect
-        assert np.allclose(np.array(resolution_function.smearing()), np.array([1.1, 2.2, 3.3, 4.4, 5.18516692]))
-
+        assert np.allclose(np.array(resolution_function.smearing()), np.array([2.51664683, 2.84038734, 3.2460762 , 3.6796519 , 4.07869271]))
 
     def test_as_dict(self):
         # When

From 876a5e4c9ad265594cc77a13c4bdb4ce0ac5bf01 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Mon, 26 May 2025 11:11:47 +0200
Subject: [PATCH 06/16] ruff fix for tests

---
 tests/model/test_resolution_functions.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/model/test_resolution_functions.py b/tests/model/test_resolution_functions.py
index ab6e0e4e..8e5d1a03 100644
--- a/tests/model/test_resolution_functions.py
+++ b/tests/model/test_resolution_functions.py
@@ -89,7 +89,8 @@ def test_constructor(self):
         resolution_function = Pointwise(q_data_points=self.data_points)
 
         # Then Expect
-        assert np.allclose(np.array(resolution_function.smearing()), np.array([2.51664683, 2.84038734, 3.2460762 , 3.6796519 , 4.07869271]))
+        assert np.allclose(np.array(resolution_function.smearing()),
+                           np.array([2.51664683, 2.84038734, 3.2460762 , 3.6796519 , 4.07869271]))
 
     def test_as_dict(self):
         # When

From 5d110a04ee8213d8c129935b7f91fa5551b416d1 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Wed, 23 Jul 2025 15:14:10 +0200
Subject: [PATCH 07/16] updated/fixed pointwise impl

---
 .../simulation/resolution_functions.ipynb     | 69 +++++++++++++++++--
 .../model/resolution_functions.py             | 23 ++-----
 src/easyreflectometry/project.py              | 21 +++---
 tests/model/test_resolution_functions.py      |  2 +-
 tests/summary/test_summary.py                 |  2 +-
 tests/test_project.py                         |  4 +-
 6 files changed, 85 insertions(+), 36 deletions(-)

diff --git a/docs/src/tutorials/simulation/resolution_functions.ipynb b/docs/src/tutorials/simulation/resolution_functions.ipynb
index 237963e7..1aca5fab 100644
--- a/docs/src/tutorials/simulation/resolution_functions.ipynb
+++ b/docs/src/tutorials/simulation/resolution_functions.ipynb
@@ -46,6 +46,7 @@
     "from easyreflectometry.model import Model\n",
     "from easyreflectometry.model import LinearSpline\n",
     "from easyreflectometry.model import PercentageFwhm\n",
+    "from easyreflectometry.model import Pointwise\n",
     "from easyreflectometry.sample import Layer\n",
     "from easyreflectometry.sample import Material\n",
     "from easyreflectometry.sample import Multilayer\n",
@@ -115,6 +116,16 @@
     "dict_reference['10'] = load(file_path_10)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e5f65ed7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dict_reference['0']"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "1ab3a164-62c8-4bd3-b0d8-e6f22c83dc74",
@@ -251,9 +262,15 @@
    "id": "defd6dd5-c618-4af6-a5c7-17532207f0a0",
    "metadata": {},
    "source": [
-    "## Resolution functions\n",
-    "\n",
-    "We now define the different resoultion functions.  "
+    "## Resolution functions "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c9d903db",
+   "metadata": {},
+   "source": [
+    "We can now define the different resoultion functions. "
    ]
   },
   {
@@ -376,11 +393,53 @@
     "plt.yscale('log')\n",
     "plt.show()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "43881642",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "key = '1'\n",
+    "reference_coords = dict_reference[key]['coords']['Qz_0'].values\n",
+    "reference_variances = dict_reference[key]['coords']['Qz_0'].variances\n",
+    "reference_data = dict_reference[key]['data']['R_0'].values\n",
+    "model_coords = np.linspace(\n",
+    "    start=min(reference_coords),\n",
+    "    stop=max(reference_coords),\n",
+    "    num=1000,\n",
+    ")\n",
+    "\n",
+    "model.resolution_function = resolution_function_dict[key]\n",
+    "model_data = model.interface().reflectity_profile(\n",
+    "    model_coords,\n",
+    "    model.unique_name,\n",
+    ")\n",
+    "plt.plot(model_coords, model_data, 'k-', label=f'Variable', linewidth=5)\n",
+    "data_points = []\n",
+    "data_points.append(reference_coords) # Qz\n",
+    "data_points.append(reference_data) # R\n",
+    "data_points.append(reference_variances) # sQz\n",
+    "model.resolution_function = Pointwise(q_data_points=data_points)\n",
+    "model_data = model.interface().reflectity_profile(\n",
+    "    model_coords,\n",
+    "    model.unique_name,\n",
+    ")\n",
+    "plt.plot(model_coords, model_data, 'r-', label=f'Pointwise')\n",
+    "\n",
+    "ax = plt.gca()\n",
+    "ax.set_xlim([-0.01, 0.45])\n",
+    "ax.set_ylim([1e-10, 2.5])\n",
+    "plt.legend()\n",
+    "plt.yscale('log')\n",
+    "plt.show()"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "easyref",
+   "display_name": "era",
    "language": "python",
    "name": "python3"
   },
@@ -394,7 +453,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.9"
+   "version": "3.12.11"
   }
  },
  "nbformat": 4,
diff --git a/src/easyreflectometry/model/resolution_functions.py b/src/easyreflectometry/model/resolution_functions.py
index 7fdf5e87..736aec21 100644
--- a/src/easyreflectometry/model/resolution_functions.py
+++ b/src/easyreflectometry/model/resolution_functions.py
@@ -31,7 +31,7 @@ def from_dict(cls, data: dict) -> ResolutionFunction:
         if data['smearing'] == 'LinearSpline':
             return LinearSpline(data['q_data_points'], data['fwhm_values'])
         if data['smearing'] == 'Pointwise':
-            return Pointwise(data['q_data_points'])
+            return Pointwise([data['q_data_points'], data['R_data_points'], data['sQz_data_points']])
         raise ValueError('Unknown resolution function type')
 
 
@@ -87,12 +87,15 @@ def smearing(self, q: Union[np.ndarray, float] = None) -> np.ndarray:
     def as_dict(
         self, skip: Optional[List[str]] = None
     ) -> dict[str, str]:  # skip is kept for consistency of the as_dict signature
-        return {'smearing': 'Pointwise', 'q_data_points': list(self.q_data_points)}
+        return {'smearing': 'Pointwise',
+                'q_data_points': list(self.q_data_points[0]),
+                'R_data_points': list(self.q_data_points[1]),
+                'sQz_data_points': list(self.q_data_points[2])}
 
     def gaussian_smearing(self, qt, Qz, R, sQz):
         weights = np.exp(-0.5 * ((qt - Qz) / sQz) ** 2)
         if np.sum(weights) == 0 or not np.isfinite(np.sum(weights)):
-            return R
+            return np.sum(R)
         weights /= (sQz * np.sqrt(2 * np.pi))
         return np.sum(R * weights) / np.sum(weights)
 
@@ -105,6 +108,7 @@ def apply_smooth_smearing(self, Qz, R, sQzs):
             R_smeared = np.zeros_like(Qz)
         else:
             R_smeared = np.zeros_like(self.q)
+
         if not isinstance(Qz, np.ndarray):
             Qz = np.array(Qz)
         if not isinstance(R, np.ndarray):
@@ -114,17 +118,4 @@ def apply_smooth_smearing(self, Qz, R, sQzs):
         for i, qt in enumerate(self.q):
             R_smeared[i] = self.gaussian_smearing(qt, Qz, R, sQzs)
 
-        # TEST LOCALLY
-        # import matplotlib.pyplot as plt
-        # plt.figure(figsize=(10, 6))
-        # plt.plot(Qz, R, label='Original R', marker='o', linestyle='none')
-        # plt.plot(self.q, R_smeared, label='Smeared R', linestyle='-')
-        # plt.yscale('log')
-        # plt.xlabel('Qz (1/angstrom)')
-        # plt.ylabel('R')
-        # plt.legend()
-        # plt.title('Original and Smeared R vs Qz (log scale)')
-        # plt.grid(True)
-        # plt.show()
-
         return R_smeared
diff --git a/src/easyreflectometry/project.py b/src/easyreflectometry/project.py
index e183ea40..66fe90c2 100644
--- a/src/easyreflectometry/project.py
+++ b/src/easyreflectometry/project.py
@@ -18,10 +18,10 @@
 from easyreflectometry.data import DataSet1D
 from easyreflectometry.data import load_as_dataset
 from easyreflectometry.fitting import MultiFitter
-from easyreflectometry.model import LinearSpline
 from easyreflectometry.model import Model
 from easyreflectometry.model import ModelCollection
 from easyreflectometry.model import PercentageFwhm
+from easyreflectometry.model import Pointwise
 from easyreflectometry.sample import Layer
 from easyreflectometry.sample import Material
 from easyreflectometry.sample import MaterialCollection
@@ -249,16 +249,15 @@ def load_experiment_for_model_at_index(self, path: Union[Path, str], index: Opti
 
         # Set the resolution function if variance data is present
         if sum(self._experiments[index].ye) != 0:
-            # q = self._experiments[index].x
-            # reflectivity = self._experiments[index].y
-            # reflectivity_error = self._experiments[index].ye
-            # q_error = self._experiments[index].xe
-            # resolution_function = Pointwise(
-            #     q_data_points=[q, reflectivity, q_error])
-            resolution_function = LinearSpline(
-                q_data_points=self._experiments[index].y,
-                fwhm_values=np.sqrt(self._experiments[index].ye),
-            )
+            q = self._experiments[index].x
+            reflectivity = self._experiments[index].y
+            q_error = self._experiments[index].xe
+            resolution_function = Pointwise(
+                q_data_points=[q, reflectivity, q_error])
+            # resolution_function = LinearSpline(
+            #     q_data_points=self._experiments[index].y,
+            #     fwhm_values=np.sqrt(self._experiments[index].ye),
+            # )
             self._models[index].resolution_function = resolution_function
 
     def sld_data_for_model_at_index(self, index: int = 0) -> DataSet1D:
diff --git a/tests/model/test_resolution_functions.py b/tests/model/test_resolution_functions.py
index 8e5d1a03..b5b1c6d7 100644
--- a/tests/model/test_resolution_functions.py
+++ b/tests/model/test_resolution_functions.py
@@ -97,7 +97,7 @@ def test_as_dict(self):
         resolution_function = Pointwise(q_data_points=self.data_points)
 
         # Then Expect
-        resolution_function.as_dict() == {'smearing': 'Pointwise', 'q_data_points': [0, 10]}
+        assert resolution_function.as_dict(), {'smearing': 'Pointwise', 'q_data_points': [0, 10]}
 
     def test_dict_round_trip(self):
         # When
diff --git a/tests/summary/test_summary.py b/tests/summary/test_summary.py
index ef8ad80e..fa018b02 100644
--- a/tests/summary/test_summary.py
+++ b/tests/summary/test_summary.py
@@ -133,7 +133,7 @@ def test_experiments_section(self, project: Project) -> None:
         assert 'No. of data points' in html
         assert '408' in html
         assert 'Resolution function' in html
-        assert 'LinearSpline' in html
+        assert 'Pointwise' in html
 
     def test_experiments_section_percentage_fhwm(self, project: Project) -> None:
         # When
diff --git a/tests/test_project.py b/tests/test_project.py
index 523138c3..d49852ce 100644
--- a/tests/test_project.py
+++ b/tests/test_project.py
@@ -12,7 +12,7 @@
 import easyreflectometry
 from easyreflectometry.data import DataSet1D
 from easyreflectometry.fitting import MultiFitter
-from easyreflectometry.model import LinearSpline
+from easyreflectometry.model import Pointwise
 from easyreflectometry.model import Model
 from easyreflectometry.model import ModelCollection
 from easyreflectometry.model import PercentageFwhm
@@ -561,7 +561,7 @@ def test_load_experiment(self):
         assert isinstance(project.experiments[5], DataSet1D)
         assert project.experiments[5].name == 'Experiment for Model 5'
         assert project.experiments[5].model == model_5
-        assert isinstance(project.models[5].resolution_function, LinearSpline)
+        assert isinstance(project.models[5].resolution_function, Pointwise)
         assert isinstance(project.models[4].resolution_function, PercentageFwhm)
 
     def test_experimental_data_at_index(self):

From c796258e62a986447759c6fa40e9a91e5ee0b98b Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Wed, 23 Jul 2025 15:19:18 +0200
Subject: [PATCH 08/16] ruff on tests

---
 tests/test_project.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_project.py b/tests/test_project.py
index d49852ce..bfa6c233 100644
--- a/tests/test_project.py
+++ b/tests/test_project.py
@@ -12,10 +12,10 @@
 import easyreflectometry
 from easyreflectometry.data import DataSet1D
 from easyreflectometry.fitting import MultiFitter
-from easyreflectometry.model import Pointwise
 from easyreflectometry.model import Model
 from easyreflectometry.model import ModelCollection
 from easyreflectometry.model import PercentageFwhm
+from easyreflectometry.model import Pointwise
 from easyreflectometry.project import Project
 from easyreflectometry.sample import Material
 from easyreflectometry.sample import MaterialCollection

From c1d9682f50b3ce6bab6c00dbf65a626f27fa3715 Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Tue, 29 Jul 2025 13:16:25 +0200
Subject: [PATCH 09/16] fix method name

---
 docs/src/tutorials/advancedfitting/multi_contrast.ipynb     | 4 ++--
 src/easyreflectometry/sample/assemblies/surfactant_layer.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/src/tutorials/advancedfitting/multi_contrast.ipynb b/docs/src/tutorials/advancedfitting/multi_contrast.ipynb
index 39c6fba5..2c812091 100644
--- a/docs/src/tutorials/advancedfitting/multi_contrast.ipynb
+++ b/docs/src/tutorials/advancedfitting/multi_contrast.ipynb
@@ -358,8 +358,8 @@
     "d83acmw.head_layer.area_per_molecule_parameter.enabled = True\n",
     "d83acmw.tail_layer.area_per_molecule_parameter.enabled = True\n",
     "\n",
-    "d70d2o.constain_multiple_contrast(d13d2o)\n",
-    "d83acmw.constain_multiple_contrast(d70d2o)"
+    "d70d2o.constrain_multiple_contrast(d13d2o)\n",
+    "d83acmw.constrain_multiple_contrast(d70d2o)"
    ]
   },
   {
diff --git a/src/easyreflectometry/sample/assemblies/surfactant_layer.py b/src/easyreflectometry/sample/assemblies/surfactant_layer.py
index a7dbe1e3..bc9df230 100644
--- a/src/easyreflectometry/sample/assemblies/surfactant_layer.py
+++ b/src/easyreflectometry/sample/assemblies/surfactant_layer.py
@@ -180,7 +180,7 @@ def constrain_solvent_roughness(self, solvent_roughness: Parameter):
         rough = ObjConstraint(solvent_roughness, '', self.tail_layer.roughness)
         self.tail_layer.roughness.user_constraints['solvent_roughness'] = rough
 
-    def constain_multiple_contrast(
+    def constrain_multiple_contrast(
         self,
         another_contrast: SurfactantLayer,
         head_layer_thickness: bool = True,

From 13cb7c5154c2be1aeb256541fc40b516fe5d0e56 Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Thu, 31 Jul 2025 13:04:18 +0200
Subject: [PATCH 10/16] datasets now have proper names, instead of `R_0` and
 `Qz_0`.

---
 src/easyreflectometry/data/__init__.py    |  2 +
 src/easyreflectometry/data/measurement.py | 53 ++++++++++++++++++++---
 tests/test_data.py                        | 28 +++++++-----
 3 files changed, 65 insertions(+), 18 deletions(-)

diff --git a/src/easyreflectometry/data/__init__.py b/src/easyreflectometry/data/__init__.py
index 26c3f270..91aab465 100644
--- a/src/easyreflectometry/data/__init__.py
+++ b/src/easyreflectometry/data/__init__.py
@@ -2,10 +2,12 @@
 from .data_store import ProjectData
 from .measurement import load
 from .measurement import load_as_dataset
+from .measurement import merge_datagroups
 
 __all__ = [
     "load",
     "load_as_dataset",
+    "merge_datagroups",
     "ProjectData",
     "DataSet1D",
 ]
diff --git a/src/easyreflectometry/data/measurement.py b/src/easyreflectometry/data/measurement.py
index 5aee6a3c..554e6e4f 100644
--- a/src/easyreflectometry/data/measurement.py
+++ b/src/easyreflectometry/data/measurement.py
@@ -1,5 +1,6 @@
 __author__ = 'github.com/arm61'
 
+import os
 from typing import TextIO
 from typing import Union
 
@@ -25,11 +26,16 @@ def load(fname: Union[TextIO, str]) -> sc.DataGroup:
 def load_as_dataset(fname: Union[TextIO, str]) -> DataSet1D:
     """Load data from an ORSO .ort file as a DataSet1D."""
     data_group = load(fname)
+    basename = os.path.splitext(os.path.basename(fname))[0]
+    data_name = 'R_' + basename
+    coords_name = 'Qz_' + basename
+    coords_name = list(data_group['coords'].keys())[0] if coords_name not in data_group['coords'] else coords_name
+    data_name = list(data_group['data'].keys())[0] if data_name not in data_group['data'] else data_name
     return DataSet1D(
-        x=data_group['coords']['Qz_0'].values,
-        y=data_group['data']['R_0'].values,
-        ye=data_group['data']['R_0'].variances,
-        xe=data_group['coords']['Qz_0'].variances,
+        x=data_group['coords'][coords_name].values,
+        y=data_group['data'][data_name].values,
+        ye=data_group['data'][data_name].variances,
+        xe=data_group['coords'][coords_name].variances,
     )
 
 
@@ -86,6 +92,8 @@ def _load_txt(fname: Union[TextIO, str]) -> sc.DataGroup:
     if ',' in first_line:
         delimiter = ','
 
+    basename = os.path.splitext(os.path.basename(fname))[0]
+
     try:
         # First load only the data to check column count
         data = np.loadtxt(fname, delimiter=delimiter, comments='#')
@@ -110,13 +118,44 @@ def _load_txt(fname: Union[TextIO, str]) -> sc.DataGroup:
         # Re-raise with more descriptive message
         raise ValueError(f"Failed to load data from {fname}: {str(error)}") from error
 
-    data = {'R_0': sc.array(dims=['Qz_0'], values=y, variances=np.square(e))}
+    data_name = 'R_' + basename
+    coords_name = 'Qz_' + basename
+    data = {data_name: sc.array(dims=[coords_name], values=y, variances=np.square(e))}
     coords = {
-        data['R_0'].dims[0]: sc.array(
-            dims=['Qz_0'],
+        data[data_name].dims[0]: sc.array(
+            dims=[coords_name],
             values=x,
             variances=np.square(xe),
             unit=sc.Unit('1/angstrom'),
         )
     }
     return sc.DataGroup(data=data, coords=coords)
+
+def merge_datagroups(*data_groups: sc.DataGroup) -> sc.DataGroup:
+    """Merge multiple DataGroups into a single DataGroup."""
+    merged_data = {}
+    merged_coords = {}
+    merged_attrs = {}
+
+    for group in data_groups:
+        for key, value in group['data'].items():
+            if key not in merged_data:
+                merged_data[key] = value
+            else:
+                merged_data[key] = sc.concatenate([merged_data[key], value])
+
+        for key, value in group['coords'].items():
+            if key not in merged_coords:
+                merged_coords[key] = value
+            else:
+                merged_coords[key] = sc.concatenate([merged_coords[key], value])
+
+        if 'attrs' not in group:
+            continue
+        for key, value in group['attrs'].items():
+            if key not in merged_attrs:
+                merged_attrs[key] = value
+            else:
+                merged_attrs[key] = {**merged_attrs[key], **value}
+
+    return sc.DataGroup(data=merged_data, coords=merged_coords, attrs=merged_attrs)
diff --git a/tests/test_data.py b/tests/test_data.py
index 9fb8e6e4..a974a75a 100644
--- a/tests/test_data.py
+++ b/tests/test_data.py
@@ -32,18 +32,22 @@ def test_load_with_txt(self):
         fpath = os.path.join(PATH_STATIC, 'test_example1.txt')
         er_data = load(fpath)
         n_data = np.loadtxt(fpath)
-        assert_almost_equal(er_data['data']['R_0'].values, n_data[:, 1])
-        assert_almost_equal(er_data['coords']['Qz_0'].values, n_data[:, 0])
-        assert_almost_equal(er_data['data']['R_0'].variances, np.square(n_data[:, 2]))
-        assert_almost_equal(er_data['coords']['Qz_0'].variances, np.square(n_data[:, 3]))
+        data_name = 'R_test_example1'
+        coords_name = 'Qz_test_example1'
+        assert_almost_equal(er_data['data'][data_name].values, n_data[:, 1])
+        assert_almost_equal(er_data['coords'][coords_name].values, n_data[:, 0])
+        assert_almost_equal(er_data['data'][data_name].variances, np.square(n_data[:, 2]))
+        assert_almost_equal(er_data['coords'][coords_name].variances, np.square(n_data[:, 3]))
 
     def test_load_with_txt_commas(self):
         fpath = os.path.join(PATH_STATIC, 'ref_concat_1.txt')
         er_data = load(fpath)
         x, y, e = np.loadtxt(fpath, delimiter=',', comments='#', unpack=True)
-        assert_almost_equal(er_data['data']['R_0'].values, y)
-        assert_almost_equal(er_data['coords']['Qz_0'].values, x)
-        assert_almost_equal(er_data['data']['R_0'].variances, np.square(e))
+        data_name = 'R_ref_concat_1'
+        coords_name = 'Qz_ref_concat_1'
+        assert_almost_equal(er_data['data'][data_name].values, y)
+        assert_almost_equal(er_data['coords'][coords_name].values, x)
+        assert_almost_equal(er_data['data'][data_name].variances, np.square(e))
 
     def test_orso1(self):
         fpath = os.path.join(PATH_STATIC, 'test_example1.ort')
@@ -93,7 +97,9 @@ def test_txt(self):
         fpath = os.path.join(PATH_STATIC, 'test_example1.txt')
         er_data = _load_txt(fpath)
         n_data = np.loadtxt(fpath)
-        assert_almost_equal(er_data['data']['R_0'].values, n_data[:, 1])
-        assert_almost_equal(er_data['coords']['Qz_0'].values, n_data[:, 0])
-        assert_almost_equal(er_data['data']['R_0'].variances, np.square(n_data[:, 2]))
-        assert_almost_equal(er_data['coords']['Qz_0'].variances, np.square(n_data[:, 3]))
+        data_name = 'R_test_example1'
+        coords_name = 'Qz_test_example1'
+        assert_almost_equal(er_data['data'][data_name].values, n_data[:, 1])
+        assert_almost_equal(er_data['coords'][coords_name].values, n_data[:, 0])
+        assert_almost_equal(er_data['data'][data_name].variances, np.square(n_data[:, 2]))
+        assert_almost_equal(er_data['coords'][coords_name].variances, np.square(n_data[:, 3]))

From c813ada60ec972f4e5150ca4faefc71a3e3457cc Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Thu, 7 Aug 2025 17:01:11 +0200
Subject: [PATCH 11/16] added color changer, renamed default model, minor fixes

---
 .../tutorials/simulation/resolution_functions.ipynb |  4 ++--
 src/easyreflectometry/fitting.py                    |  3 ++-
 src/easyreflectometry/model/model.py                |  7 ++++---
 src/easyreflectometry/model/model_collection.py     |  7 ++++---
 src/easyreflectometry/project.py                    | 13 ++++++++++++-
 tests/model/test_model.py                           |  6 +++---
 tests/model/test_model_collection.py                |  8 ++++----
 tests/summary/test_summary.py                       |  2 +-
 tests/test_project.py                               |  4 ++--
 9 files changed, 34 insertions(+), 20 deletions(-)

diff --git a/docs/src/tutorials/simulation/resolution_functions.ipynb b/docs/src/tutorials/simulation/resolution_functions.ipynb
index 1aca5fab..4fc42ad2 100644
--- a/docs/src/tutorials/simulation/resolution_functions.ipynb
+++ b/docs/src/tutorials/simulation/resolution_functions.ipynb
@@ -439,7 +439,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "era",
+   "display_name": "erl",
    "language": "python",
    "name": "python3"
   },
@@ -453,7 +453,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.12.10"
   }
  },
  "nbformat": 4,
diff --git a/src/easyreflectometry/fitting.py b/src/easyreflectometry/fitting.py
index c7bb75c5..41cf72ba 100644
--- a/src/easyreflectometry/fitting.py
+++ b/src/easyreflectometry/fitting.py
@@ -50,7 +50,8 @@ def fit(self, data: sc.DataGroup, id: int = 0) -> sc.DataGroup:
             )
             sld_profile = self.easy_science_multi_fitter._fit_objects[i].interface.sld_profile(self._models[i].unique_name)
             new_data[f'SLD_{id}'] = sc.array(dims=[f'z_{id}'], values=sld_profile[1] * 1e-6, unit=sc.Unit('1/angstrom') ** 2)
-            new_data['attrs'][f'R_{id}_model'] = {'model': sc.scalar(self._models[i].as_dict())}
+            if 'attrs' in new_data:
+                new_data['attrs'][f'R_{id}_model'] = {'model': sc.scalar(self._models[i].as_dict())}
             new_data['coords'][f'z_{id}'] = sc.array(
                 dims=[f'z_{id}'], values=sld_profile[0], unit=(1 / new_data['coords'][f'Qz_{id}'].unit).unit
             )
diff --git a/src/easyreflectometry/model/model.py b/src/easyreflectometry/model/model.py
index 969c955a..32242a3e 100644
--- a/src/easyreflectometry/model/model.py
+++ b/src/easyreflectometry/model/model.py
@@ -42,6 +42,7 @@
     },
 }
 
+COLORS =["#0173B2", "#DE8F05", "#029E73", "#D55E00", "#CC78BC", "#CA9161", "#FBAFE4", "#949494", "#ECE133", "#56B4E9"]
 
 class Model(BaseObj):
     """Model is the class that represents the experiment.
@@ -60,8 +61,8 @@ def __init__(
         scale: Union[Parameter, Number, None] = None,
         background: Union[Parameter, Number, None] = None,
         resolution_function: Union[ResolutionFunction, None] = None,
-        name: str = 'EasyModel',
-        color: str = 'black',
+        name: str = 'Model',
+        color: str = COLORS[0],
         unique_name: Optional[str] = None,
         interface=None,
     ):
@@ -70,7 +71,7 @@ def __init__(
         :param sample: The sample being modelled.
         :param scale: Scaling factor of profile.
         :param background: Linear background magnitude.
-        :param name: Name of the model, defaults to 'EasyModel'.
+        :param name: Name of the model, defaults to 'Model'.
         :param resolution_function: Resolution function, defaults to PercentageFwhm.
         :param interface: Calculator interface, defaults to `None`.
 
diff --git a/src/easyreflectometry/model/model_collection.py b/src/easyreflectometry/model/model_collection.py
index 7ae3b9f2..7e9435ed 100644
--- a/src/easyreflectometry/model/model_collection.py
+++ b/src/easyreflectometry/model/model_collection.py
@@ -5,7 +5,7 @@
 from typing import Tuple
 
 from easyreflectometry.sample.collections.base_collection import BaseCollection
-
+from easyreflectometry.model.model import COLORS
 from .model import Model
 
 
@@ -18,7 +18,7 @@ class ModelCollection(BaseCollection):
     def __init__(
         self,
         *models: Tuple[Model],
-        name: str = 'EasyModels',
+        name: str = 'Models',
         interface=None,
         unique_name: Optional[str] = None,
         populate_if_none: bool = True,
@@ -41,7 +41,8 @@ def add_model(self, model: Optional[Model] = None):
         :param model: Model to add.
         """
         if model is None:
-            model = Model(name='EasyModel added', interface=self.interface)
+            color = COLORS[len(self) % len(COLORS)]
+            model = Model(name='Model', interface=self.interface, color=color)
         self.append(model)
 
     def duplicate_model(self, index: int):
diff --git a/src/easyreflectometry/project.py b/src/easyreflectometry/project.py
index 66fe90c2..a8d09c92 100644
--- a/src/easyreflectometry/project.py
+++ b/src/easyreflectometry/project.py
@@ -240,9 +240,20 @@ def get_index_d2o(self) -> int:
             self._materials.add_material(Material(name='D2O', sld=6.36, isld=0.0))
         return [material.name for material in self._materials].index('D2O')
 
+    def load_new_experiment(self, path: Union[Path, str]) -> None:
+        new_experiment = load_as_dataset(str(path))
+        new_index = len(self._experiments)
+        new_experiment.name = f'Experiment {new_index}'
+        model_index = 0
+        if new_index < len(self.models):
+            model_index = new_index
+        new_experiment.model = self.models[model_index]
+        self._experiments[new_index] = new_experiment
+        # self._current_model_index = new_index
+
     def load_experiment_for_model_at_index(self, path: Union[Path, str], index: Optional[int] = 0) -> None:
         self._experiments[index] = load_as_dataset(str(path))
-        self._experiments[index].name = f'Experiment for Model {index}'
+        self._experiments[index].name = f'Experiment {index}'
         self._experiments[index].model = self.models[index]
 
         self._with_experiments = True
diff --git a/tests/model/test_model.py b/tests/model/test_model.py
index 45755e25..4c8171a0 100644
--- a/tests/model/test_model.py
+++ b/tests/model/test_model.py
@@ -30,7 +30,7 @@
 class TestModel(unittest.TestCase):
     def test_default(self):
         p = Model()
-        assert_equal(p.name, 'EasyModel')
+        assert_equal(p.name, 'Model')
         assert_equal(p.interface, None)
         assert_equal(p.sample.name, 'EasySample')
         assert_equal(p.scale.display_name, 'scale')
@@ -389,7 +389,7 @@ def test_repr(self):
 
         assert (
             model.__repr__()
-            == 'EasyModel:\n  scale: 1.0\n  background: 1.0e-08\n  resolution: 5.0 %\n  color: black\n  sample:\n    EasySample:\n    - EasyMultilayer:\n        EasyLayerCollection:\n        - EasyLayer:\n            material:\n              EasyMaterial:\n                sld: 4.186e-6 1/Å^2\n                isld: 0.000e-6 1/Å^2\n            thickness: 10.000 Å\n            roughness: 3.300 Å\n    - EasyMultilayer:\n        EasyLayerCollection:\n        - EasyLayer:\n            material:\n              EasyMaterial:\n                sld: 4.186e-6 1/Å^2\n                isld: 0.000e-6 1/Å^2\n            thickness: 10.000 Å\n            roughness: 3.300 Å\n'  # noqa: E501
+            == "Model:\n  scale: 1.0\n  background: 1.0e-08\n  resolution: 5.0 %\n  color: '#0173B2'\n  sample:\n    EasySample:\n    - EasyMultilayer:\n        EasyLayerCollection:\n        - EasyLayer:\n            material:\n              EasyMaterial:\n                sld: 4.186e-6 1/Å^2\n                isld: 0.000e-6 1/Å^2\n            thickness: 10.000 Å\n            roughness: 3.300 Å\n    - EasyMultilayer:\n        EasyLayerCollection:\n        - EasyLayer:\n            material:\n              EasyMaterial:\n                sld: 4.186e-6 1/Å^2\n                isld: 0.000e-6 1/Å^2\n            thickness: 10.000 Å\n            roughness: 3.300 Å\n"  # noqa: E501
         )
 
     def test_repr_resolution_function(self):
@@ -398,7 +398,7 @@ def test_repr_resolution_function(self):
         model.resolution_function = resolution_function
         assert (
             model.__repr__()
-            == 'EasyModel:\n  scale: 1.0\n  background: 1.0e-08\n  resolution: function of Q\n  color: black\n  sample:\n    EasySample:\n    - EasyMultilayer:\n        EasyLayerCollection:\n        - EasyLayer:\n            material:\n              EasyMaterial:\n                sld: 4.186e-6 1/Å^2\n                isld: 0.000e-6 1/Å^2\n            thickness: 10.000 Å\n            roughness: 3.300 Å\n    - EasyMultilayer:\n        EasyLayerCollection:\n        - EasyLayer:\n            material:\n              EasyMaterial:\n                sld: 4.186e-6 1/Å^2\n                isld: 0.000e-6 1/Å^2\n            thickness: 10.000 Å\n            roughness: 3.300 Å\n'  # noqa: E501
+            == "Model:\n  scale: 1.0\n  background: 1.0e-08\n  resolution: function of Q\n  color: '#0173B2'\n  sample:\n    EasySample:\n    - EasyMultilayer:\n        EasyLayerCollection:\n        - EasyLayer:\n            material:\n              EasyMaterial:\n                sld: 4.186e-6 1/Å^2\n                isld: 0.000e-6 1/Å^2\n            thickness: 10.000 Å\n            roughness: 3.300 Å\n    - EasyMultilayer:\n        EasyLayerCollection:\n        - EasyLayer:\n            material:\n              EasyMaterial:\n                sld: 4.186e-6 1/Å^2\n                isld: 0.000e-6 1/Å^2\n            thickness: 10.000 Å\n            roughness: 3.300 Å\n"  # noqa: E501
         )
 
 
diff --git a/tests/model/test_model_collection.py b/tests/model/test_model_collection.py
index 9ab03475..7b22f12b 100644
--- a/tests/model/test_model_collection.py
+++ b/tests/model/test_model_collection.py
@@ -10,14 +10,14 @@ def test_default(self):
         collection = ModelCollection()
 
         # Expect
-        assert collection.name == 'EasyModels'
+        assert collection.name == 'Models'
         assert collection.interface is None
         assert len(collection) == 1
-        assert collection[0].name == 'EasyModel'
+        assert collection[0].name == 'Model'
 
     def test_dont_populate(self):
         p = ModelCollection(populate_if_none=False)
-        assert p.name == 'EasyModels'
+        assert p.name == 'Models'
         assert p.interface is None
         assert len(p) == 0
 
@@ -31,7 +31,7 @@ def test_from_pars(self):
         collection = ModelCollection(model_1, model_2, model_3)
 
         # Expect
-        assert collection.name == 'EasyModels'
+        assert collection.name == 'Models'
         assert collection.interface is None
         assert len(collection) == 3
         assert collection[0].name == 'Model1'
diff --git a/tests/summary/test_summary.py b/tests/summary/test_summary.py
index fa018b02..bcd898e1 100644
--- a/tests/summary/test_summary.py
+++ b/tests/summary/test_summary.py
@@ -129,7 +129,7 @@ def test_experiments_section(self, project: Project) -> None:
         html = summary._experiments_section()
 
         # Expect
-        assert 'Experiment for Model 0' in html
+        assert 'Experiment 0' in html
         assert 'No. of data points' in html
         assert '408' in html
         assert 'Resolution function' in html
diff --git a/tests/test_project.py b/tests/test_project.py
index bfa6c233..d9202de8 100644
--- a/tests/test_project.py
+++ b/tests/test_project.py
@@ -559,7 +559,7 @@ def test_load_experiment(self):
         # Expect
         assert list(project.experiments.keys()) == [5]
         assert isinstance(project.experiments[5], DataSet1D)
-        assert project.experiments[5].name == 'Experiment for Model 5'
+        assert project.experiments[5].name == 'Experiment 5'
         assert project.experiments[5].model == model_5
         assert isinstance(project.models[5].resolution_function, Pointwise)
         assert isinstance(project.models[4].resolution_function, PercentageFwhm)
@@ -575,7 +575,7 @@ def test_experimental_data_at_index(self):
         data = project.experimental_data_for_model_at_index()
 
         # Expect
-        assert data.name == 'Experiment for Model 0'
+        assert data.name == 'Experiment 0'
         assert data.is_experiment
         assert isinstance(data, DataSet1D)
         assert len(data.x) == 408

From a4a1b9d9d32d59a61e968d433e7e32ed34460827 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Fri, 8 Aug 2025 08:53:02 +0200
Subject: [PATCH 12/16] fix ruff, fix test name

---
 src/easyreflectometry/model/model_collection.py  | 3 ++-
 tests/sample/assemblies/test_surfactant_layer.py | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/easyreflectometry/model/model_collection.py b/src/easyreflectometry/model/model_collection.py
index 7e9435ed..02c5e5db 100644
--- a/src/easyreflectometry/model/model_collection.py
+++ b/src/easyreflectometry/model/model_collection.py
@@ -4,8 +4,9 @@
 from typing import Optional
 from typing import Tuple
 
-from easyreflectometry.sample.collections.base_collection import BaseCollection
 from easyreflectometry.model.model import COLORS
+from easyreflectometry.sample.collections.base_collection import BaseCollection
+
 from .model import Model
 
 
diff --git a/tests/sample/assemblies/test_surfactant_layer.py b/tests/sample/assemblies/test_surfactant_layer.py
index b6b25243..8b47c34e 100644
--- a/tests/sample/assemblies/test_surfactant_layer.py
+++ b/tests/sample/assemblies/test_surfactant_layer.py
@@ -81,7 +81,7 @@ def test_conformal_roughness(self):
         assert p.tail_layer.roughness.value == 4
         assert p.head_layer.roughness.value == 4
 
-    def test_constain_solvent_roughness(self):
+    def test_constrain_solvent_roughness(self):
         p = SurfactantLayer()
         layer = Layer()
         p.tail_layer.roughness.value = 2

From 0dc62dcec5e6a7dc7ace2d6f9997cc922367cd3c Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Fri, 8 Aug 2025 14:32:52 +0200
Subject: [PATCH 13/16] added experiment index

---
 src/easyreflectometry/project.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/src/easyreflectometry/project.py b/src/easyreflectometry/project.py
index a8d09c92..1ec3a77c 100644
--- a/src/easyreflectometry/project.py
+++ b/src/easyreflectometry/project.py
@@ -56,6 +56,7 @@ def __init__(self):
         self._current_assembly_index = 0
         self._current_layer_index = 0
         self._fitter_model_index = None
+        self._current_experiment_index = 0
 
         # Project flags
         self._created = False
@@ -155,6 +156,19 @@ def current_layer_index(self, value: int) -> None:
         if self._current_layer_index != value:
             self._current_layer_index = value
 
+    @property
+    def current_experiment_index(self) -> Optional[int]:
+        return self._current_experiment_index
+
+    @current_experiment_index.setter
+    def current_experiment_index(self, value: int) -> None:
+        if value < 0 or value >= len(self._experiments):
+            raise ValueError(f'Index {value} out of range')
+        if self._current_experiment_index != value:
+            self._current_experiment_index = value
+            # Resetting the model index to 0 when changing the experiment
+            #self.current_model_index = 0
+
     @property
     def created(self) -> bool:
         return self._created

From 86219e6893960fd7327a55aba92d5c8e143bf52b Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Fri, 8 Aug 2025 14:39:16 +0200
Subject: [PATCH 14/16] added tests

---
 tests/test_project.py | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/tests/test_project.py b/tests/test_project.py
index d9202de8..6e0172a8 100644
--- a/tests/test_project.py
+++ b/tests/test_project.py
@@ -634,3 +634,39 @@ def test_parameters(self):
         # Expect
         assert len(parameters) == 14
         assert isinstance(parameters[0], Parameter)
+
+    def test_current_experiment_index_getter_and_setter(self):
+        project = Project()
+        # Default value should be 0
+        assert project.current_experiment_index == 0
+
+        # Add two experiments to allow setting index 1
+        project._experiments[0] = DataSet1D(name="exp0", x=[], y=[], ye=[], xe=[], model=None)
+        project._experiments[1] = DataSet1D(name="exp1", x=[], y=[], ye=[], xe=[], model=None)
+
+        # Set to 1 (valid)
+        project.current_experiment_index = 1
+        assert project.current_experiment_index == 1
+
+        # Set to 0 (valid)
+        project.current_experiment_index = 0
+        assert project.current_experiment_index == 0
+
+    def test_current_experiment_index_setter_out_of_range(self):
+        project = Project()
+        # Add one experiment
+        project._experiments[0] = DataSet1D(name="exp0", x=[], y=[], ye=[], xe=[], model=None)
+
+        # Negative index should raise
+        try:
+            project.current_experiment_index = -1
+            assert False, "Expected ValueError for negative index"
+        except ValueError:
+            pass
+
+        # Index >= len(_experiments) should raise
+        try:
+            project.current_experiment_index = 1
+            assert False, "Expected ValueError for out-of-range index"
+        except ValueError:
+            pass

From aed1629883ef4cb1e8ccc6151df36d6e40d6a288 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Fri, 15 Aug 2025 11:11:55 +0200
Subject: [PATCH 15/16] fix issue with multiple experiments and a single model

---
 src/easyreflectometry/summary/summary.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/easyreflectometry/summary/summary.py b/src/easyreflectometry/summary/summary.py
index 4ac259e0..23c3261c 100644
--- a/src/easyreflectometry/summary/summary.py
+++ b/src/easyreflectometry/summary/summary.py
@@ -143,9 +143,9 @@ def _experiments_section(self) -> str:
         for idx, experiment in self._project.experiments.items():
             experiment_name = experiment.name
             num_data_points = len(experiment.x)
-            resolution_function = self._project.models[idx].resolution_function.as_dict()['smearing']
+            resolution_function = experiment.model.resolution_function.as_dict()['smearing']
             if resolution_function == 'PercentageFwhm':
-                precentage = self._project.models[idx].resolution_function.as_dict()['constant']
+                precentage = experiment.model.resolution_function.as_dict()['constant']
                 resolution_function = f'{resolution_function} {precentage}%'
             range_min = min(experiment.y)
             range_max = max(experiment.y)

From c73638bf96fe039796b799b63a06b3967e460fe9 Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Tue, 19 Aug 2025 08:41:29 +0200
Subject: [PATCH 16/16] added a helper method

---
 src/easyreflectometry/project.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/easyreflectometry/project.py b/src/easyreflectometry/project.py
index 1ec3a77c..e4846cef 100644
--- a/src/easyreflectometry/project.py
+++ b/src/easyreflectometry/project.py
@@ -79,6 +79,12 @@ def parameters(self) -> List[Parameter]:
                 parameters.append(vertice_obj)
         return parameters
 
+    @property
+    def enabled_parameters(self) -> List[Parameter]:
+        parameters = self.parameters
+        # Only include enabled parameters
+        return [param for param in parameters if param.enabled]
+
     @property
     def q_min(self):
         if self._q_min is None: