From d66a0a09b16c0a1249a8dc621c0000606e7e697b Mon Sep 17 00:00:00 2001
From: Eric Lindgren <ericlin@chalmers.se>
Date: Thu, 27 Mar 2025 17:22:33 +0100
Subject: [PATCH 01/14] add first example of experimental weighting

---
 examples/joint-refinement_weighting.py       | 102 +++++++++++++++++++
 src/easydiffraction/analysis/minimization.py |   6 +-
 2 files changed, 107 insertions(+), 1 deletion(-)
 create mode 100644 examples/joint-refinement_weighting.py

diff --git a/examples/joint-refinement_weighting.py b/examples/joint-refinement_weighting.py
new file mode 100644
index 00000000..ff46ddcd
--- /dev/null
+++ b/examples/joint-refinement_weighting.py
@@ -0,0 +1,102 @@
+
+"""
+Joint Refinement Example (Advanced API)
+
+This example demonstrates a more flexible and advanced usage of the EasyDiffraction
+library by explicitly creating and configuring some objects. It is more suitable for
+users comfortable with Python programming and those interested in custom workflows.
+"""
+
+from easydiffraction import (
+    Project,
+    SampleModel,
+    Experiment
+)
+
+# Create and configure sample model
+
+model = SampleModel("pbso4")
+model.space_group.name.value = "P n m a"
+model.cell.length_a.value = 8.5
+model.cell.length_b.value = 5.35
+model.cell.length_c.value = 6.9
+model.atom_sites.add("Pb", "Pb", 0.1876, 0.25, 0.167, b_iso=1.37)
+model.atom_sites.add("S", "S", 0.0654, 0.25, 0.684, b_iso=0.3777)
+model.atom_sites.add("O1", "O", 0.9082, 0.25, 0.5954, b_iso=1.9764)
+model.atom_sites.add("O2", "O", 0.1935, 0.25, 0.5432, b_iso=1.4456)
+model.atom_sites.add("O3", "O", 0.0811, 0.0272, 0.8086, b_iso=1.2822)
+
+# Create and configure experiments
+
+# Experiment 1: Neutron powder diffraction
+expt1 = Experiment(id="npd", radiation_probe="neutron", data_path="examples/data/pbso4_powder_neutron_cw.dat")
+expt1.instr_setup.wavelength = 1.91
+expt1.instr_calib.twotheta_offset = -0.1406
+expt1.peak_broad.gauss_u = 0.139
+expt1.peak_broad.gauss_v = -0.412
+expt1.peak_broad.gauss_w = 0.386
+expt1.peak_broad.lorentz_x = 0
+expt1.peak_broad.lorentz_y = 0.088
+expt1.linked_phases.add("pbso4", scale=1.0)
+for x, y in [
+    (11.0, 206.1624),
+    (15.0, 194.75),
+    (20.0, 194.505),
+    (30.0, 188.4375),
+    (50.0, 207.7633),
+    (70.0, 201.7002),
+    (120.0, 244.4525),
+    (153.0, 226.0595),
+]:
+    expt1.background.add(x, y)
+
+# Experiment 2: X-ray powder diffraction
+expt2 = Experiment(id="xrd", radiation_probe="xray", data_path="examples/data/pbso4_powder_xray.dat")
+expt2.instr_setup.wavelength = 1.540567
+expt2.instr_calib.twotheta_offset = -0.05181
+expt2.peak_broad.gauss_u = 0.304138
+expt2.peak_broad.gauss_v = -0.112622
+expt2.peak_broad.gauss_w = 0.021272
+expt2.peak_broad.lorentz_x = 0
+expt2.peak_broad.lorentz_y = 0.057691
+expt2.linked_phases.add("pbso4", scale=0.005)
+for x, y in [
+    (11.0, 141.8516),
+    (13.0, 102.8838),
+    (16.0, 78.0551),
+    (20.0, 124.0121),
+    (30.0, 123.7123),
+    (50.0, 120.8266),
+    (90.0, 113.7473),
+    (110.0, 132.4643),
+]:
+    expt2.background.add(x, y)
+
+# Create project and add sample model and experiments
+project = Project()
+project.sample_models.add(model)
+project.experiments.add(expt1)
+project.experiments.add(expt2)
+
+# Weight the experiments
+expt1.weight = 0.4
+expt2.weight = 0.6
+
+# Set calculator, minimizer and refinement strategy
+project.analysis.current_calculator = "cryspy"
+project.analysis.current_minimizer = "lmfit (leastsq)"
+project.analysis.refinement_strategy = 'combined'
+
+# Define free parameters
+model.cell.length_a.free = True
+model.cell.length_b.free = True
+model.cell.length_c.free = True
+expt1.linked_phases["pbso4"].scale.free = True
+expt2.linked_phases["pbso4"].scale.free = True
+
+# Run refinement
+project.analysis.fit()
+
+project.analysis.show_meas_vs_calc_chart(expt_id="npd", x_min=62, x_max=66, show_residual=True)
+project.analysis.show_meas_vs_calc_chart(expt_id="xrd", x_min=26, x_max=28, show_residual=True)
+
diff --git a/src/easydiffraction/analysis/minimization.py b/src/easydiffraction/analysis/minimization.py
index 495e103f..08c71725 100644
--- a/src/easydiffraction/analysis/minimization.py
+++ b/src/easydiffraction/analysis/minimization.py
@@ -58,12 +58,16 @@ def _residual_function(self, engine_params, parameters, sample_models, experimen
         # Sync parameters back to objects
         self.minimizer._sync_result_to_parameters(parameters, engine_params)
 
+        weights = np.array([getattr(experiment, 'weight', 1.0) for experiment in experiments._items.values()], dtype=np.float64)
+        weights /= np.sum(weights)  # Normalize weights so they sum to 1
+
         residuals = []
-        for expt_id, experiment in experiments._items.items():
+        for (expt_id, experiment), weight in zip(experiments._items.items(), weights):
             y_calc = calculator.calculate_pattern(sample_models, experiment)
             y_meas = experiment.datastore.pattern.meas
             y_meas_su = experiment.datastore.pattern.meas_su
             diff = (y_meas - y_calc) / y_meas_su
+            diff *= weight
             residuals.extend(diff)
 
         residuals = np.array(residuals)

From c1fd60d98c83a88d7b5341d07a94293533b86976 Mon Sep 17 00:00:00 2001
From: Eric Lindgren <ericlin@chalmers.se>
Date: Fri, 28 Mar 2025 14:58:01 +0100
Subject: [PATCH 02/14] scale expected chi squared by a factor of 4, since
 default weighting impacts chi squared

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

diff --git a/tests/functional_test/fitting/test_fitting.py b/tests/functional_test/fitting/test_fitting.py
index a2d15c93..43496187 100644
--- a/tests/functional_test/fitting/test_fitting.py
+++ b/tests/functional_test/fitting/test_fitting.py
@@ -88,7 +88,7 @@ def test_joint_fit_neutron_xray_pd_cwl_pbso4() -> None:
     project.analysis.fit()
 
     # Assert results
-    assert_almost_equal(project.analysis.fit_results.reduced_chi_square, 21.1, decimal=1)
+    assert_almost_equal(project.analysis.fit_results.reduced_chi_square, 5.32, decimal=1)
 
 
 if __name__ == '__main__':

From 58b7120db120cb631ab020e139c872b0ce54b7af Mon Sep 17 00:00:00 2001
From: Eric Lindgren <ericlin@chalmers.se>
Date: Wed, 2 Apr 2025 16:58:39 +0200
Subject: [PATCH 03/14] play around with joint_fit api; currently using ID of
 experiment as key for weights

---
 examples/joint-refinement_weighting.py       | 58 +++++++++-----------
 src/easydiffraction/analysis/analysis.py     |  6 +-
 src/easydiffraction/analysis/minimization.py |  9 ++-
 3 files changed, 35 insertions(+), 38 deletions(-)

diff --git a/examples/joint-refinement_weighting.py b/examples/joint-refinement_weighting.py
index ff46ddcd..0178a54b 100644
--- a/examples/joint-refinement_weighting.py
+++ b/examples/joint-refinement_weighting.py
@@ -1,4 +1,3 @@
-
 """
 Joint Refinement Example (Advanced API)
 
@@ -30,14 +29,15 @@
 
 # Experiment 1: Neutron powder diffraction
 expt1 = Experiment(id="npd", radiation_probe="neutron", data_path="examples/data/pbso4_powder_neutron_cw.dat")
-expt1.instr_setup.wavelength = 1.91
-expt1.instr_calib.twotheta_offset = -0.1406
-expt1.peak_broad.gauss_u = 0.139
-expt1.peak_broad.gauss_v = -0.412
-expt1.peak_broad.gauss_w = 0.386
-expt1.peak_broad.lorentz_x = 0
-expt1.peak_broad.lorentz_y = 0.088
+expt1.instrument.setup_wavelength = 1.91
+expt1.instrument.calib_twotheta_offset = -0.1406
+expt1.peak.broad_gauss_u = 0.139
+expt1.peak.broad_gauss_v = -0.412
+expt1.peak.broad_gauss_w = 0.386
+expt1.peak.broad_lorentz_x = 0
+expt1.peak.broad_lorentz_y = 0.088
 expt1.linked_phases.add("pbso4", scale=1.0)
+expt1.background_type = "line-segment"
 for x, y in [
     (11.0, 206.1624),
     (15.0, 194.75),
@@ -52,23 +52,22 @@
 
 # Experiment 2: X-ray powder diffraction
 expt2 = Experiment(id="xrd", radiation_probe="xray", data_path="examples/data/pbso4_powder_xray.dat")
-expt2.instr_setup.wavelength = 1.540567
-expt2.instr_calib.twotheta_offset = -0.05181
-expt2.peak_broad.gauss_u = 0.304138
-expt2.peak_broad.gauss_v = -0.112622
-expt2.peak_broad.gauss_w = 0.021272
-expt2.peak_broad.lorentz_x = 0
-expt2.peak_broad.lorentz_y = 0.057691
+expt2.instrument.setup_wavelength = 1.540567
+expt2.instrument.calib_twotheta_offset = -0.05181
+expt2.peak.broad_gauss_u = 0.304138
+expt2.peak.broad_gauss_v = -0.112622
+expt2.peak.broad_gauss_w = 0.021272
+expt2.peak.broad_lorentz_x = 0
+expt2.peak.broad_lorentz_y = 0.057691
 expt2.linked_phases.add("pbso4", scale=0.005)
+expt2.background_type = "chebyshev polynomial"
 for x, y in [
-    (11.0, 141.8516),
-    (13.0, 102.8838),
-    (16.0, 78.0551),
-    (20.0, 124.0121),
-    (30.0, 123.7123),
-    (50.0, 120.8266),
-    (90.0, 113.7473),
-    (110.0, 132.4643),
+    (0, 119.195),
+    (1, 6.221),
+    (2, -45.725),
+    (3, 8.119),
+    (4, 54.552),
+    (5, -20.661),
 ]:
     expt2.background.add(x, y)
 
@@ -78,14 +77,14 @@
 project.experiments.add(expt1)
 project.experiments.add(expt2)
 
-# Weight the experiments
-expt1.weight = 0.4
-expt2.weight = 0.6
-
 # Set calculator, minimizer and refinement strategy
 project.analysis.current_calculator = "cryspy"
 project.analysis.current_minimizer = "lmfit (leastsq)"
-project.analysis.refinement_strategy = 'combined'
+project.analysis.fit_mode = 'joint'
+# project.analysis.joint_fit.add("expt1", weight=0.4)  # Default weight could be 0.5
+# project.analysis.joint_fit.add("expt2", weight=0.6)  # Default weight could be 0.5
+project.analysis.joint_fit.setdefault("xrd",0.4)  # Default weight could be 0.5
+project.analysis.joint_fit.setdefault("npd",0.6)  # Default weight could be 0.5
 
 # Define free parameters
 model.cell.length_a.free = True
@@ -97,6 +96,3 @@
 # Run refinement
 project.analysis.fit()
 
-project.analysis.show_meas_vs_calc_chart(expt_id="npd", x_min=62, x_max=66, show_residual=True)
-project.analysis.show_meas_vs_calc_chart(expt_id="xrd", x_min=26, x_max=28, show_residual=True)
-
diff --git a/src/easydiffraction/analysis/analysis.py b/src/easydiffraction/analysis/analysis.py
index 71c5d4be..0e86185f 100644
--- a/src/easydiffraction/analysis/analysis.py
+++ b/src/easydiffraction/analysis/analysis.py
@@ -117,6 +117,8 @@ def fit_mode(self, strategy):
         if strategy not in ['single', 'joint']:
             raise ValueError("Fit mode must be either 'single' or 'joint'")
         self._fit_mode = strategy
+        if strategy == 'joint':
+            self.joint_fit = {}
         print(paragraph("Current ffit mode changed to"))
         print(self._fit_mode)
 
@@ -215,7 +217,7 @@ def fit(self):
 
         if self.fit_mode == 'joint':
             print(paragraph(f"Using all experiments 🔬 {experiment_ids} for '{self.fit_mode}' fitting"))
-            self.fitter.fit(sample_models, experiments, calculator)
+            self.fitter.fit(sample_models, experiments, calculator, weights=self.joint_fit)
         elif self.fit_mode == 'single':
             for expt_id in list(experiments._items.keys()):
                 print(paragraph(f"Using experiment 🔬 '{expt_id}' for '{self.fit_mode}' fitting"))
@@ -248,4 +250,4 @@ def show_as_cif(self):
         print(paragraph(f"Analysis 🧮 info as cif"))
         print(top)
         print("\n".join(padded_lines))
-        print(bottom)
\ No newline at end of file
+        print(bottom)
diff --git a/src/easydiffraction/analysis/minimization.py b/src/easydiffraction/analysis/minimization.py
index 08c71725..d39158c9 100644
--- a/src/easydiffraction/analysis/minimization.py
+++ b/src/easydiffraction/analysis/minimization.py
@@ -14,7 +14,7 @@ def __init__(self, selection: str = 'lmfit (leastsq)'):
         self.minimizer = MinimizerFactory.create_minimizer(selection)
         self.results = None
 
-    def fit(self, sample_models, experiments, calculator):
+    def fit(self, sample_models, experiments, calculator, weights=None):
         """
         Run the fitting process.
         """
@@ -27,7 +27,7 @@ def fit(self, sample_models, experiments, calculator):
         for parameter in parameters:
             parameter.start_value = parameter.value
 
-        objective_function = lambda engine_params: self._residual_function(engine_params, parameters, sample_models, experiments, calculator)
+        objective_function = lambda engine_params: self._residual_function(engine_params, parameters, sample_models, experiments, calculator, weights)
 
         # Perform fitting
         self.results = self.minimizer.fit(parameters, objective_function)
@@ -50,15 +50,14 @@ def _process_fit_results(self, sample_models, experiments, calculator):
     def _collect_free_parameters(self, sample_models, experiments):
         return sample_models.get_free_params() + experiments.get_free_params()
 
-    def _residual_function(self, engine_params, parameters, sample_models, experiments, calculator):
+    def _residual_function(self, engine_params, parameters, sample_models, experiments, calculator, weights=None):
         """
         Residual function computes the difference between measured and calculated patterns.
         It updates the parameter values according to the optimizer-provided engine_params.
         """
         # Sync parameters back to objects
         self.minimizer._sync_result_to_parameters(parameters, engine_params)
-
-        weights = np.array([getattr(experiment, 'weight', 1.0) for experiment in experiments._items.values()], dtype=np.float64)
+        weights = np.ones(len(experiments)) if weights is None else np.array([getattr(weights, experiment_name, 1.0) for experiment_name in experiments._items.keys()], dtype=np.float64)
         weights /= np.sum(weights)  # Normalize weights so they sum to 1
 
         residuals = []

From 54184b31fd644d045d72a0d34899e01d3142c003 Mon Sep 17 00:00:00 2001
From: Eric Lindgren <ericlin@chalmers.se>
Date: Thu, 3 Apr 2025 10:34:45 +0200
Subject: [PATCH 04/14] take the square root of weights so that they enter
 linearly into reduced chi-squared

---
 src/easydiffraction/analysis/minimization.py  | 9 ++++++---
 tests/functional_test/fitting/test_fitting.py | 2 +-
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/src/easydiffraction/analysis/minimization.py b/src/easydiffraction/analysis/minimization.py
index d39158c9..6cc49926 100644
--- a/src/easydiffraction/analysis/minimization.py
+++ b/src/easydiffraction/analysis/minimization.py
@@ -57,8 +57,11 @@ def _residual_function(self, engine_params, parameters, sample_models, experimen
         """
         # Sync parameters back to objects
         self.minimizer._sync_result_to_parameters(parameters, engine_params)
-        weights = np.ones(len(experiments)) if weights is None else np.array([getattr(weights, experiment_name, 1.0) for experiment_name in experiments._items.keys()], dtype=np.float64)
-        weights /= np.sum(weights)  # Normalize weights so they sum to 1
+        
+        # Prepare weights for joint fitting
+        N_experiments = len(experiments._items.keys())
+        weights = np.ones(N_experiments) if weights is None else np.array([getattr(weights, experiment_name, 1.0) for experiment_name in experiments._items.keys()], dtype=np.float64)
+        weights *= N_experiments / np.sum(weights)  # Normalize weights so they sum to N, where N is the number of experiments
 
         residuals = []
         for (expt_id, experiment), weight in zip(experiments._items.items(), weights):
@@ -66,7 +69,7 @@ def _residual_function(self, engine_params, parameters, sample_models, experimen
             y_meas = experiment.datastore.pattern.meas
             y_meas_su = experiment.datastore.pattern.meas_su
             diff = (y_meas - y_calc) / y_meas_su
-            diff *= weight
+            diff *= np.sqrt(weight)  # Residuls are squared before going into reduced chi-squared
             residuals.extend(diff)
 
         residuals = np.array(residuals)
diff --git a/tests/functional_test/fitting/test_fitting.py b/tests/functional_test/fitting/test_fitting.py
index 43496187..a2d15c93 100644
--- a/tests/functional_test/fitting/test_fitting.py
+++ b/tests/functional_test/fitting/test_fitting.py
@@ -88,7 +88,7 @@ def test_joint_fit_neutron_xray_pd_cwl_pbso4() -> None:
     project.analysis.fit()
 
     # Assert results
-    assert_almost_equal(project.analysis.fit_results.reduced_chi_square, 5.32, decimal=1)
+    assert_almost_equal(project.analysis.fit_results.reduced_chi_square, 21.1, decimal=1)
 
 
 if __name__ == '__main__':

From 95828c63a517243b75fd6f59512b479bf867c859 Mon Sep 17 00:00:00 2001
From: Eric Lindgren <ericlin@chalmers.se>
Date: Thu, 3 Apr 2025 10:50:57 +0200
Subject: [PATCH 05/14] automatically create the joint fit object, with 0.5 as
 default weight

---
 src/easydiffraction/analysis/analysis.py       | 4 ++--
 src/easydiffraction/analysis/minimization.py   | 4 ++--
 src/easydiffraction/experiments/experiments.py | 4 ++++
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/easydiffraction/analysis/analysis.py b/src/easydiffraction/analysis/analysis.py
index 0e86185f..0ccfd13a 100644
--- a/src/easydiffraction/analysis/analysis.py
+++ b/src/easydiffraction/analysis/analysis.py
@@ -118,8 +118,8 @@ def fit_mode(self, strategy):
             raise ValueError("Fit mode must be either 'single' or 'joint'")
         self._fit_mode = strategy
         if strategy == 'joint':
-            self.joint_fit = {}
-        print(paragraph("Current ffit mode changed to"))
+            self.joint_fit = { id: 0.5 for id in self.project.experiments.ids }  # Pre-populate with all experiments 
+        print(paragraph("Current fit mode changed to"))
         print(self._fit_mode)
 
     def show_available_fit_modes(self):
diff --git a/src/easydiffraction/analysis/minimization.py b/src/easydiffraction/analysis/minimization.py
index 6cc49926..e96dd211 100644
--- a/src/easydiffraction/analysis/minimization.py
+++ b/src/easydiffraction/analysis/minimization.py
@@ -59,8 +59,8 @@ def _residual_function(self, engine_params, parameters, sample_models, experimen
         self.minimizer._sync_result_to_parameters(parameters, engine_params)
         
         # Prepare weights for joint fitting
-        N_experiments = len(experiments._items.keys())
-        weights = np.ones(N_experiments) if weights is None else np.array([getattr(weights, experiment_name, 1.0) for experiment_name in experiments._items.keys()], dtype=np.float64)
+        N_experiments = len(experiments.ids)
+        weights = np.ones(N_experiments) if weights is None else np.array([getattr(weights, id, 1.0) for id in experiments.ids], dtype=np.float64)
         weights *= N_experiments / np.sum(weights)  # Normalize weights so they sum to N, where N is the number of experiments
 
         residuals = []
diff --git a/src/easydiffraction/experiments/experiments.py b/src/easydiffraction/experiments/experiments.py
index 14b7bf86..38a5358d 100644
--- a/src/easydiffraction/experiments/experiments.py
+++ b/src/easydiffraction/experiments/experiments.py
@@ -90,6 +90,10 @@ def show_ids(self):
         print(paragraph("Defined experiments" + " 🔬"))
         print(list(self._experiments.keys()))
 
+    @property
+    def ids(self):
+        return list(self._experiments.keys())
+
     def show_params(self):
         for exp in self._experiments.values():
             print(exp)

From 753a612c36bc3753da9220bb76466b5dc70b6e4a Mon Sep 17 00:00:00 2001
From: Eric Lindgren <ericlin@chalmers.se>
Date: Thu, 3 Apr 2025 11:03:25 +0200
Subject: [PATCH 06/14] use a sum of weights to 1 instead of N

---
 src/easydiffraction/analysis/minimization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/easydiffraction/analysis/minimization.py b/src/easydiffraction/analysis/minimization.py
index e96dd211..e3536042 100644
--- a/src/easydiffraction/analysis/minimization.py
+++ b/src/easydiffraction/analysis/minimization.py
@@ -61,7 +61,7 @@ def _residual_function(self, engine_params, parameters, sample_models, experimen
         # Prepare weights for joint fitting
         N_experiments = len(experiments.ids)
         weights = np.ones(N_experiments) if weights is None else np.array([getattr(weights, id, 1.0) for id in experiments.ids], dtype=np.float64)
-        weights *= N_experiments / np.sum(weights)  # Normalize weights so they sum to N, where N is the number of experiments
+        weights /= np.sum(weights)  # Normalize weights so they sum to 1
 
         residuals = []
         for (expt_id, experiment), weight in zip(experiments._items.items(), weights):

From 521070e0eb753839dcb0ee407861bf3e562d919c Mon Sep 17 00:00:00 2001
From: Eric Lindgren <ericlin@chalmers.se>
Date: Thu, 3 Apr 2025 14:03:50 +0200
Subject: [PATCH 07/14] update test to actually set the joint_fit object

---
 src/easydiffraction/analysis/analysis.py      | 1 +
 src/easydiffraction/analysis/minimization.py  | 8 ++++----
 tests/functional_test/fitting/test_fitting.py | 4 +++-
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/easydiffraction/analysis/analysis.py b/src/easydiffraction/analysis/analysis.py
index 0ccfd13a..89833955 100644
--- a/src/easydiffraction/analysis/analysis.py
+++ b/src/easydiffraction/analysis/analysis.py
@@ -217,6 +217,7 @@ def fit(self):
 
         if self.fit_mode == 'joint':
             print(paragraph(f"Using all experiments 🔬 {experiment_ids} for '{self.fit_mode}' fitting"))
+            print(self.joint_fit)
             self.fitter.fit(sample_models, experiments, calculator, weights=self.joint_fit)
         elif self.fit_mode == 'single':
             for expt_id in list(experiments._items.keys()):
diff --git a/src/easydiffraction/analysis/minimization.py b/src/easydiffraction/analysis/minimization.py
index e3536042..be2d4b4b 100644
--- a/src/easydiffraction/analysis/minimization.py
+++ b/src/easydiffraction/analysis/minimization.py
@@ -60,11 +60,11 @@ def _residual_function(self, engine_params, parameters, sample_models, experimen
         
         # Prepare weights for joint fitting
         N_experiments = len(experiments.ids)
-        weights = np.ones(N_experiments) if weights is None else np.array([getattr(weights, id, 1.0) for id in experiments.ids], dtype=np.float64)
-        weights /= np.sum(weights)  # Normalize weights so they sum to 1
-
+        _weights = np.ones(N_experiments) if weights is None else np.array([weights.get(id, 1.0) for id in experiments.ids], dtype=np.float64)
+        _weights /= np.sum(_weights)  # Normalize weights so they sum to 1
         residuals = []
-        for (expt_id, experiment), weight in zip(experiments._items.items(), weights):
+
+        for (expt_id, experiment), weight in zip(experiments._items.items(), _weights):
             y_calc = calculator.calculate_pattern(sample_models, experiment)
             y_meas = experiment.datastore.pattern.meas
             y_meas_su = experiment.datastore.pattern.meas_su
diff --git a/tests/functional_test/fitting/test_fitting.py b/tests/functional_test/fitting/test_fitting.py
index a2d15c93..121be94c 100644
--- a/tests/functional_test/fitting/test_fitting.py
+++ b/tests/functional_test/fitting/test_fitting.py
@@ -76,6 +76,8 @@ def test_joint_fit_neutron_xray_pd_cwl_pbso4() -> None:
     project.analysis.current_calculator = "cryspy"
     project.analysis.current_minimizer = "lmfit (leastsq)"
     project.analysis.fit_mode = 'joint'
+    project.analysis.joint_fit['xrd'] = 0.3
+    project.analysis.joint_fit['npd'] = 0.7
 
     # Define free parameters
     model.cell.length_a.free = True
@@ -88,7 +90,7 @@ def test_joint_fit_neutron_xray_pd_cwl_pbso4() -> None:
     project.analysis.fit()
 
     # Assert results
-    assert_almost_equal(project.analysis.fit_results.reduced_chi_square, 21.1, decimal=1)
+    assert_almost_equal(project.analysis.fit_results.reduced_chi_square, 7.2, decimal=1)
 
 
 if __name__ == '__main__':

From de4331029b4aa6e07822c685f87fa6aca770f78a Mon Sep 17 00:00:00 2001
From: Andrew Sazonov <andrew.sazonov@icloud.com>
Date: Mon, 7 Apr 2025 10:22:11 +0200
Subject: [PATCH 08/14] Adds two new examples to show expected GOF in joint fit

---
 .../pbso4_powder_neutron_cw_first-half.dat    | 1800 ++++++++++
 .../data/pbso4_powder_neutron_cw_full.dat     | 2910 +++++++++++++++++
 .../pbso4_powder_neutron_cw_second-half.dat   | 1110 +++++++
 examples/joint-fit_single-dataset.py          |   77 +
 examples/joint-fit_split-single-dataset.py    |  104 +
 5 files changed, 6001 insertions(+)
 create mode 100644 examples/data/pbso4_powder_neutron_cw_first-half.dat
 create mode 100644 examples/data/pbso4_powder_neutron_cw_full.dat
 create mode 100644 examples/data/pbso4_powder_neutron_cw_second-half.dat
 create mode 100644 examples/joint-fit_single-dataset.py
 create mode 100644 examples/joint-fit_split-single-dataset.py

diff --git a/examples/data/pbso4_powder_neutron_cw_first-half.dat b/examples/data/pbso4_powder_neutron_cw_first-half.dat
new file mode 100644
index 00000000..00310507
--- /dev/null
+++ b/examples/data/pbso4_powder_neutron_cw_first-half.dat
@@ -0,0 +1,1800 @@
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diff --git a/examples/data/pbso4_powder_neutron_cw_full.dat b/examples/data/pbso4_powder_neutron_cw_full.dat
new file mode 100644
index 00000000..b775a9cc
--- /dev/null
+++ b/examples/data/pbso4_powder_neutron_cw_full.dat
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diff --git a/examples/data/pbso4_powder_neutron_cw_second-half.dat b/examples/data/pbso4_powder_neutron_cw_second-half.dat
new file mode 100644
index 00000000..c5308303
--- /dev/null
+++ b/examples/data/pbso4_powder_neutron_cw_second-half.dat
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diff --git a/examples/joint-fit_single-dataset.py b/examples/joint-fit_single-dataset.py
new file mode 100644
index 00000000..7eef5041
--- /dev/null
+++ b/examples/joint-fit_single-dataset.py
@@ -0,0 +1,77 @@
+"""
+Joint Refinement Example (Advanced API)
+
+This example demonstrates a more flexible and advanced usage of the EasyDiffraction
+library by explicitly creating and configuring some objects. It is more suitable for
+users comfortable with Python programming and those interested in custom workflows.
+"""
+from numpy.testing import assert_almost_equal
+
+from easydiffraction import (
+    Project,
+    SampleModel,
+    Experiment
+)
+
+# Create and configure sample model
+
+model = SampleModel("pbso4")
+model.space_group.name.value = "P n m a"
+model.cell.length_a.value = 8.4693
+model.cell.length_b.value = 5.3910
+model.cell.length_c.value = 6.9506
+model.atom_sites.add("Pb", "Pb", 0.1876, 0.25, 0.167, b_iso=1.37)
+model.atom_sites.add("S", "S", 0.0654, 0.25, 0.684, b_iso=0.3777)
+model.atom_sites.add("O1", "O", 0.9082, 0.25, 0.5954, b_iso=1.9764)
+model.atom_sites.add("O2", "O", 0.1935, 0.25, 0.5432, b_iso=1.4456)
+model.atom_sites.add("O3", "O", 0.0811, 0.0272, 0.8086, b_iso=1.2822)
+
+# Create and configure experiments
+
+# Experiment: Neutron powder diffraction (full dataset)
+expt = Experiment(id="npd", radiation_probe="neutron", data_path="examples/data/pbso4_powder_neutron_cw_full.dat")
+expt.instrument.setup_wavelength = 1.91
+expt.instrument.calib_twotheta_offset = -0.1406
+expt.peak.broad_gauss_u = 0.139
+expt.peak.broad_gauss_v = -0.4124
+expt.peak.broad_gauss_w = 0.386
+expt.peak.broad_lorentz_x = 0
+expt.peak.broad_lorentz_y = 0.0878
+expt.linked_phases.add("pbso4", scale=1.46)
+expt.background_type = "line-segment"
+for x, y in [
+    (11.0, 206.1624),
+    (15.0, 194.75),
+    (20.0, 194.505),
+    (30.0, 188.4375),
+    (50.0, 207.7633),
+    (70.0, 201.7002),
+    (120.0, 244.4525),
+    (153.0, 226.0595),
+]:
+    expt.background.add(x, y)
+
+# Create project and add sample model and experiments
+project = Project()
+project.sample_models.add(model)
+project.experiments.add(expt)
+
+# Set calculator, minimizer and refinement strategy
+project.analysis.current_calculator = "cryspy"
+project.analysis.current_minimizer = "lmfit (leastsq)"
+project.analysis.fit_mode = 'joint'
+# project.analysis.joint_fit.add("expt1", weight=0.4)  # Default weight could be 0.5
+# project.analysis.joint_fit.add("expt2", weight=0.6)  # Default weight could be 0.5
+project.analysis.joint_fit.setdefault("npd1", 0.5)  # Default weight could be 0.5
+project.analysis.joint_fit.setdefault("npd2", 0.5)  # Default weight could be 0.5
+
+# Define free parameters
+model.cell.length_a.free = True
+model.cell.length_b.free = True
+model.cell.length_c.free = True
+
+# Run refinement
+project.analysis.fit()
+
+# Assert results
+assert_almost_equal(project.analysis.fit_results.reduced_chi_square, 4.66, decimal=1)
diff --git a/examples/joint-fit_split-single-dataset.py b/examples/joint-fit_split-single-dataset.py
new file mode 100644
index 00000000..89799a37
--- /dev/null
+++ b/examples/joint-fit_split-single-dataset.py
@@ -0,0 +1,104 @@
+"""
+Joint Refinement Example (Advanced API)
+
+This example demonstrates a more flexible and advanced usage of the EasyDiffraction
+library by explicitly creating and configuring some objects. It is more suitable for
+users comfortable with Python programming and those interested in custom workflows.
+"""
+from numpy.testing import assert_almost_equal
+
+from easydiffraction import (
+    Project,
+    SampleModel,
+    Experiment
+)
+
+# Create and configure sample model
+
+model = SampleModel("pbso4")
+model.space_group.name.value = "P n m a"
+model.cell.length_a.value = 8.4693
+model.cell.length_b.value = 5.3910
+model.cell.length_c.value = 6.9506
+model.atom_sites.add("Pb", "Pb", 0.1876, 0.25, 0.167, b_iso=1.37)
+model.atom_sites.add("S", "S", 0.0654, 0.25, 0.684, b_iso=0.3777)
+model.atom_sites.add("O1", "O", 0.9082, 0.25, 0.5954, b_iso=1.9764)
+model.atom_sites.add("O2", "O", 0.1935, 0.25, 0.5432, b_iso=1.4456)
+model.atom_sites.add("O3", "O", 0.0811, 0.0272, 0.8086, b_iso=1.2822)
+
+# Create and configure experiments
+
+# Experiment 1: Neutron powder diffraction (first half of the dataset)
+expt1 = Experiment(id="npd1", radiation_probe="neutron", data_path="examples/data/pbso4_powder_neutron_cw_first-half.dat")
+expt1.instrument.setup_wavelength = 1.91
+expt1.instrument.calib_twotheta_offset = -0.1406
+expt1.peak.broad_gauss_u = 0.139
+expt1.peak.broad_gauss_v = -0.4124
+expt1.peak.broad_gauss_w = 0.386
+expt1.peak.broad_lorentz_x = 0
+expt1.peak.broad_lorentz_y = 0.0878
+expt1.linked_phases.add("pbso4", scale=1.46)
+expt1.background_type = "line-segment"
+for x, y in [
+    (11.0, 206.1624),
+    (15.0, 194.75),
+    (20.0, 194.505),
+    (30.0, 188.4375),
+    (50.0, 207.7633),
+    (70.0, 201.7002),
+    (120.0, 244.4525),
+    (153.0, 226.0595),
+]:
+    expt1.background.add(x, y)
+
+# Experiment 2: Neutron powder diffraction (second half of the dataset)
+expt2 = Experiment(id="npd2", radiation_probe="neutron", data_path="examples/data/pbso4_powder_neutron_cw_second-half.dat")
+expt2.instrument.setup_wavelength = 1.91
+expt2.instrument.calib_twotheta_offset = -0.1406
+expt2.peak.broad_gauss_u = 0.139
+expt2.peak.broad_gauss_v = -0.4124
+expt2.peak.broad_gauss_w = 0.386
+expt2.peak.broad_lorentz_x = 0
+expt2.peak.broad_lorentz_y = 0.0878
+expt2.linked_phases.add("pbso4", scale=1.46)
+expt2.background_type = "line-segment"
+for x, y in [
+    (11.0, 206.1624),
+    (15.0, 194.75),
+    (20.0, 194.505),
+    (30.0, 188.4375),
+    (50.0, 207.7633),
+    (70.0, 201.7002),
+    (120.0, 244.4525),
+    (153.0, 226.0595),
+]:
+    expt2.background.add(x, y)
+
+# Create project and add sample model and experiments
+project = Project()
+project.sample_models.add(model)
+project.experiments.add(expt1)
+project.experiments.add(expt2)
+
+# Set calculator, minimizer and refinement strategy
+project.analysis.current_calculator = "cryspy"
+project.analysis.current_minimizer = "lmfit (leastsq)"
+project.analysis.fit_mode = 'joint'
+# project.analysis.joint_fit.add("expt1", weight=0.4)  # Default weight could be 0.5
+# project.analysis.joint_fit.add("expt2", weight=0.6)  # Default weight could be 0.5
+project.analysis.joint_fit.setdefault("npd1", 0.5)  # Default weight could be 0.5
+project.analysis.joint_fit.setdefault("npd2", 0.5)  # Default weight could be 0.5
+
+# Define free parameters
+model.cell.length_a.free = True
+model.cell.length_b.free = True
+model.cell.length_c.free = True
+#expt1.linked_phases["pbso4"].scale.free = True
+#expt2.linked_phases["pbso4"].scale.free = True
+
+# Run refinement
+project.analysis.fit()
+
+# Assert results
+assert_almost_equal(project.analysis.fit_results.reduced_chi_square, 4.66, decimal=1)
+

From cf13aaf208232bb33dcf6ec25d8dc07b3abaa7c7 Mon Sep 17 00:00:00 2001
From: Eric Lindgren <ericlin@chalmers.se>
Date: Mon, 7 Apr 2025 11:53:29 +0200
Subject: [PATCH 09/14] increase expected chi_squred to expected value when
 fitting multiple experiments

---
 src/easydiffraction/analysis/analysis.py      | 1 -
 src/easydiffraction/analysis/minimization.py  | 6 +++++-
 tests/functional_test/fitting/test_fitting.py | 2 +-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/easydiffraction/analysis/analysis.py b/src/easydiffraction/analysis/analysis.py
index 89833955..0ccfd13a 100644
--- a/src/easydiffraction/analysis/analysis.py
+++ b/src/easydiffraction/analysis/analysis.py
@@ -217,7 +217,6 @@ def fit(self):
 
         if self.fit_mode == 'joint':
             print(paragraph(f"Using all experiments 🔬 {experiment_ids} for '{self.fit_mode}' fitting"))
-            print(self.joint_fit)
             self.fitter.fit(sample_models, experiments, calculator, weights=self.joint_fit)
         elif self.fit_mode == 'single':
             for expt_id in list(experiments._items.keys()):
diff --git a/src/easydiffraction/analysis/minimization.py b/src/easydiffraction/analysis/minimization.py
index be2d4b4b..b3ee34e0 100644
--- a/src/easydiffraction/analysis/minimization.py
+++ b/src/easydiffraction/analysis/minimization.py
@@ -61,7 +61,11 @@ def _residual_function(self, engine_params, parameters, sample_models, experimen
         # Prepare weights for joint fitting
         N_experiments = len(experiments.ids)
         _weights = np.ones(N_experiments) if weights is None else np.array([weights.get(id, 1.0) for id in experiments.ids], dtype=np.float64)
-        _weights /= np.sum(_weights)  # Normalize weights so they sum to 1
+        # Normalize weights so they sum to N_experiments
+        # We should obtain the same reduced chi_squared when a single dataset is split into
+        # two parts and fit together. If weights sum to one, then reduced chi_squared
+        # will be half as large as expected.
+        _weights *= N_experiments / np.sum(_weights)   
         residuals = []
 
         for (expt_id, experiment), weight in zip(experiments._items.items(), _weights):
diff --git a/tests/functional_test/fitting/test_fitting.py b/tests/functional_test/fitting/test_fitting.py
index 121be94c..ee8d8719 100644
--- a/tests/functional_test/fitting/test_fitting.py
+++ b/tests/functional_test/fitting/test_fitting.py
@@ -90,7 +90,7 @@ def test_joint_fit_neutron_xray_pd_cwl_pbso4() -> None:
     project.analysis.fit()
 
     # Assert results
-    assert_almost_equal(project.analysis.fit_results.reduced_chi_square, 7.2, decimal=1)
+    assert_almost_equal(project.analysis.fit_results.reduced_chi_square, 14.4, decimal=1)
 
 
 if __name__ == '__main__':

From aa8393248fd1165a783b0b9ac3562ae6645ef4d0 Mon Sep 17 00:00:00 2001
From: Eric Lindgren <ericlin@chalmers.se>
Date: Mon, 7 Apr 2025 14:17:36 +0200
Subject: [PATCH 10/14] make better use of ids property

---
 src/easydiffraction/analysis/analysis.py       | 5 +++--
 src/easydiffraction/experiments/experiments.py | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/easydiffraction/analysis/analysis.py b/src/easydiffraction/analysis/analysis.py
index f7a54236..e8ed732e 100644
--- a/src/easydiffraction/analysis/analysis.py
+++ b/src/easydiffraction/analysis/analysis.py
@@ -119,7 +119,8 @@ def fit_mode(self, strategy):
             raise ValueError("Fit mode must be either 'single' or 'joint'")
         self._fit_mode = strategy
         if strategy == 'joint':
-            self.joint_fit = { id: 0.5 for id in self.project.experiments.ids }  # Pre-populate with all experiments 
+            if self.joint_fit is None:
+                self.joint_fit = { id: 0.5 for id in self.project.experiments.ids }  # Pre-populate with all experiments 
         print(paragraph("Current fit mode changed to"))
         print(self._fit_mode)
 
@@ -214,7 +215,7 @@ def fit(self):
             return
 
         # Run the fitting process
-        experiment_ids = list(experiments._items.keys())
+        experiment_ids = experiments.ids
 
         if self.fit_mode == 'joint':
             print(paragraph(f"Using all experiments 🔬 {experiment_ids} for '{self.fit_mode}' fitting"))
diff --git a/src/easydiffraction/experiments/experiments.py b/src/easydiffraction/experiments/experiments.py
index 38a5358d..8d7aba2a 100644
--- a/src/easydiffraction/experiments/experiments.py
+++ b/src/easydiffraction/experiments/experiments.py
@@ -88,7 +88,7 @@ def remove(self, experiment_id):
 
     def show_ids(self):
         print(paragraph("Defined experiments" + " 🔬"))
-        print(list(self._experiments.keys()))
+        print(self.ids)
 
     @property
     def ids(self):

From 60755810599467d218c43cf505bde25af972cd2f Mon Sep 17 00:00:00 2001
From: Eric Lindgren <ericlin@chalmers.se>
Date: Mon, 7 Apr 2025 15:06:52 +0200
Subject: [PATCH 11/14] use hasattr to check for existance of ids

---
 src/easydiffraction/analysis/analysis.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/easydiffraction/analysis/analysis.py b/src/easydiffraction/analysis/analysis.py
index e8ed732e..2f429f88 100644
--- a/src/easydiffraction/analysis/analysis.py
+++ b/src/easydiffraction/analysis/analysis.py
@@ -119,7 +119,7 @@ def fit_mode(self, strategy):
             raise ValueError("Fit mode must be either 'single' or 'joint'")
         self._fit_mode = strategy
         if strategy == 'joint':
-            if self.joint_fit is None:
+            if not hasattr(self, 'joint_fit'):
                 self.joint_fit = { id: 0.5 for id in self.project.experiments.ids }  # Pre-populate with all experiments 
         print(paragraph("Current fit mode changed to"))
         print(self._fit_mode)

From 1ebc89337a7a7e34912b107ca8ce13b7619036e1 Mon Sep 17 00:00:00 2001
From: Andrew Sazonov <andrew.sazonov@icloud.com>
Date: Mon, 7 Apr 2025 16:09:15 +0200
Subject: [PATCH 12/14] Updates data paths

---
 examples/joint-refinement_weighting.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/joint-refinement_weighting.py b/examples/joint-refinement_weighting.py
index 0178a54b..15c76cf1 100644
--- a/examples/joint-refinement_weighting.py
+++ b/examples/joint-refinement_weighting.py
@@ -28,7 +28,7 @@
 # Create and configure experiments
 
 # Experiment 1: Neutron powder diffraction
-expt1 = Experiment(id="npd", radiation_probe="neutron", data_path="examples/data/pbso4_powder_neutron_cw.dat")
+expt1 = Experiment(id="npd", radiation_probe="neutron", data_path="examples/data/d1a_pbso4.dat")
 expt1.instrument.setup_wavelength = 1.91
 expt1.instrument.calib_twotheta_offset = -0.1406
 expt1.peak.broad_gauss_u = 0.139
@@ -51,7 +51,7 @@
     expt1.background.add(x, y)
 
 # Experiment 2: X-ray powder diffraction
-expt2 = Experiment(id="xrd", radiation_probe="xray", data_path="examples/data/pbso4_powder_xray.dat")
+expt2 = Experiment(id="xrd", radiation_probe="xray", data_path="examples/data/lab_pbso4.dat")
 expt2.instrument.setup_wavelength = 1.540567
 expt2.instrument.calib_twotheta_offset = -0.05181
 expt2.peak.broad_gauss_u = 0.304138

From 7962ca76ecb0191c717cda726aa35cdb523d40db Mon Sep 17 00:00:00 2001
From: Eric Lindgren <ericlin@chalmers.se>
Date: Tue, 8 Apr 2025 15:47:06 +0200
Subject: [PATCH 13/14] fix issue where joint_fit was not updated because of
 setdefault

---
 examples/joint-fit_split-single-dataset.py       |  4 ++--
 src/easydiffraction/analysis/analysis.py         |  1 +
 src/easydiffraction/analysis/minimization.py     |  2 +-
 tests/functional_tests/fitting/test_joint-fit.py | 10 +++++++++-
 4 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/examples/joint-fit_split-single-dataset.py b/examples/joint-fit_split-single-dataset.py
index 89799a37..18485f71 100644
--- a/examples/joint-fit_split-single-dataset.py
+++ b/examples/joint-fit_split-single-dataset.py
@@ -86,8 +86,8 @@
 project.analysis.fit_mode = 'joint'
 # project.analysis.joint_fit.add("expt1", weight=0.4)  # Default weight could be 0.5
 # project.analysis.joint_fit.add("expt2", weight=0.6)  # Default weight could be 0.5
-project.analysis.joint_fit.setdefault("npd1", 0.5)  # Default weight could be 0.5
-project.analysis.joint_fit.setdefault("npd2", 0.5)  # Default weight could be 0.5
+project.analysis.joint_fit["npd1"] = 0.5  # Default weight could be 0.5
+project.analysis.joint_fit["npd2"] = 0.5  # Default weight could be 0.5
 
 # Define free parameters
 model.cell.length_a.free = True
diff --git a/src/easydiffraction/analysis/analysis.py b/src/easydiffraction/analysis/analysis.py
index 2f429f88..2e396d9a 100644
--- a/src/easydiffraction/analysis/analysis.py
+++ b/src/easydiffraction/analysis/analysis.py
@@ -120,6 +120,7 @@ def fit_mode(self, strategy):
         self._fit_mode = strategy
         if strategy == 'joint':
             if not hasattr(self, 'joint_fit'):
+                print("resetting joint_fit")
                 self.joint_fit = { id: 0.5 for id in self.project.experiments.ids }  # Pre-populate with all experiments 
         print(paragraph("Current fit mode changed to"))
         print(self._fit_mode)
diff --git a/src/easydiffraction/analysis/minimization.py b/src/easydiffraction/analysis/minimization.py
index b8d44998..6dadde99 100644
--- a/src/easydiffraction/analysis/minimization.py
+++ b/src/easydiffraction/analysis/minimization.py
@@ -57,7 +57,7 @@ def _residual_function(self, engine_params, parameters, sample_models, experimen
         """
         # Sync parameters back to objects
         self.minimizer._sync_result_to_parameters(parameters, engine_params)
-        
+
         # Prepare weights for joint fitting
         N_experiments = len(experiments.ids)
         _weights = np.ones(N_experiments) if weights is None else np.array([weights.get(id, 1.0) for id in experiments.ids], dtype=np.float64)
diff --git a/tests/functional_tests/fitting/test_joint-fit.py b/tests/functional_tests/fitting/test_joint-fit.py
index 81f2f265..2e7b6f54 100644
--- a/tests/functional_tests/fitting/test_joint-fit.py
+++ b/tests/functional_tests/fitting/test_joint-fit.py
@@ -1,4 +1,5 @@
 from numpy.testing import assert_almost_equal
+from numpy import isclose
 
 from easydiffraction import (
     Project,
@@ -92,8 +93,15 @@ def test_joint_fit_neutron_xray_pd_cwl_pbso4() -> None:
     project.analysis.show_meas_vs_calc_chart(expt_id="xrd", x_min=26, x_max=28, show_residual=True)
 
     # Compare fit quality
-    assert_almost_equal(project.analysis.fit_results.reduced_chi_square, 14.4, decimal=1)
+    chi_squared = project.analysis.fit_results.reduced_chi_square
+    assert_almost_equal(chi_squared, 14.4, decimal=1)
 
+    # Results should be different if weights are changed
+    project.analysis.joint_fit['xrd'] = 0.9
+    project.analysis.joint_fit['npd'] = 0.1
 
+    project.analysis.fit()
+    assert not isclose(chi_squared, 14.4)
+    
 if __name__ == '__main__':
     test_joint_fit_neutron_xray_pd_cwl_pbso4()

From 67025514b7214d66d2e0074e970fe7211b4a19f1 Mon Sep 17 00:00:00 2001
From: Eric Lindgren <ericlin@chalmers.se>
Date: Tue, 8 Apr 2025 16:23:36 +0200
Subject: [PATCH 14/14] implement JointFitExperiments as a container for
 experiments and associated weights

---
 examples/joint-fit_split-single-dataset.py    |  5 ++--
 src/easydiffraction/analysis/analysis.py      | 11 ++++---
 .../analysis/joint_fit_experiments.py         | 29 +++++++++++++++++++
 src/easydiffraction/analysis/minimization.py  |  2 +-
 .../fitting/test_joint-fit.py                 |  8 ++---
 5 files changed, 44 insertions(+), 11 deletions(-)
 create mode 100644 src/easydiffraction/analysis/joint_fit_experiments.py

diff --git a/examples/joint-fit_split-single-dataset.py b/examples/joint-fit_split-single-dataset.py
index 18485f71..57eda27d 100644
--- a/examples/joint-fit_split-single-dataset.py
+++ b/examples/joint-fit_split-single-dataset.py
@@ -86,8 +86,9 @@
 project.analysis.fit_mode = 'joint'
 # project.analysis.joint_fit.add("expt1", weight=0.4)  # Default weight could be 0.5
 # project.analysis.joint_fit.add("expt2", weight=0.6)  # Default weight could be 0.5
-project.analysis.joint_fit["npd1"] = 0.5  # Default weight could be 0.5
-project.analysis.joint_fit["npd2"] = 0.5  # Default weight could be 0.5
+print(project.analysis.joint_fit_experiments["npd1"])
+project.analysis.joint_fit_experiments["npd1"] = 0.5  # Default weight could be 0.5
+project.analysis.joint_fit_experiments["npd2"] = 0.5  # Default weight could be 0.5
 
 # Define free parameters
 model.cell.length_a.free = True
diff --git a/src/easydiffraction/analysis/analysis.py b/src/easydiffraction/analysis/analysis.py
index 2e396d9a..99f38e18 100644
--- a/src/easydiffraction/analysis/analysis.py
+++ b/src/easydiffraction/analysis/analysis.py
@@ -8,6 +8,7 @@
 from .calculators.calculator_factory import CalculatorFactory
 from .minimization import DiffractionMinimizer
 from .minimizers.minimizer_factory import MinimizerFactory
+from .joint_fit_experiments import JointFitExperiments
 
 
 class Analysis:
@@ -119,9 +120,11 @@ def fit_mode(self, strategy):
             raise ValueError("Fit mode must be either 'single' or 'joint'")
         self._fit_mode = strategy
         if strategy == 'joint':
-            if not hasattr(self, 'joint_fit'):
-                print("resetting joint_fit")
-                self.joint_fit = { id: 0.5 for id in self.project.experiments.ids }  # Pre-populate with all experiments 
+            if not hasattr(self, 'joint_fit_experiments'):
+                # Pre-populate all experiments with weight 0.5
+                self.joint_fit_experiments = JointFitExperiments()
+                for id in self.project.experiments.ids:
+                    self.joint_fit_experiments.add(id, weight=0.5)
         print(paragraph("Current fit mode changed to"))
         print(self._fit_mode)
 
@@ -220,7 +223,7 @@ def fit(self):
 
         if self.fit_mode == 'joint':
             print(paragraph(f"Using all experiments 🔬 {experiment_ids} for '{self.fit_mode}' fitting"))
-            self.fitter.fit(sample_models, experiments, calculator, weights=self.joint_fit)
+            self.fitter.fit(sample_models, experiments, calculator, weights=self.joint_fit_experiments)
         elif self.fit_mode == 'single':
             for expt_id in list(experiments._items.keys()):
                 print(paragraph(f"Using experiment 🔬 '{expt_id}' for '{self.fit_mode}' fitting"))
diff --git a/src/easydiffraction/analysis/joint_fit_experiments.py b/src/easydiffraction/analysis/joint_fit_experiments.py
new file mode 100644
index 00000000..06a3a1c0
--- /dev/null
+++ b/src/easydiffraction/analysis/joint_fit_experiments.py
@@ -0,0 +1,29 @@
+from easydiffraction.core.collection import Collection
+from easydiffraction.core.parameter import Descriptor
+
+class JointFitExperiments(Collection):
+    """
+    Collection manager for experiments that are fitted together
+    in a `joint` fit.
+    """
+    def __init__(self):
+        super().__init__()
+
+    def add(self, id: str, weight: float):
+        """Add an experiment with it's associated weight"""
+        # Save both id and weight as immutable Descriptors
+        self.id = Descriptor(
+            value=id,
+            cif_name="id"
+        )
+        self.weight = Descriptor(
+            value=weight,
+            cif_name="weight"
+        )
+        self._items[id] = weight
+
+    def __getitem__(self, key):
+        return self._items[key]
+
+    def __setitem__(self, key, value):
+        self._items[key] = value
diff --git a/src/easydiffraction/analysis/minimization.py b/src/easydiffraction/analysis/minimization.py
index 6dadde99..90fabc01 100644
--- a/src/easydiffraction/analysis/minimization.py
+++ b/src/easydiffraction/analysis/minimization.py
@@ -60,7 +60,7 @@ def _residual_function(self, engine_params, parameters, sample_models, experimen
 
         # Prepare weights for joint fitting
         N_experiments = len(experiments.ids)
-        _weights = np.ones(N_experiments) if weights is None else np.array([weights.get(id, 1.0) for id in experiments.ids], dtype=np.float64)
+        _weights = np.ones(N_experiments) if weights is None else np.array([weights._items.get(id, 1.0) for id in experiments.ids], dtype=np.float64)
         # Normalize weights so they sum to N_experiments
         # We should obtain the same reduced chi_squared when a single dataset is split into
         # two parts and fit together. If weights sum to one, then reduced chi_squared
diff --git a/tests/functional_tests/fitting/test_joint-fit.py b/tests/functional_tests/fitting/test_joint-fit.py
index 2e7b6f54..67248177 100644
--- a/tests/functional_tests/fitting/test_joint-fit.py
+++ b/tests/functional_tests/fitting/test_joint-fit.py
@@ -77,8 +77,8 @@ def test_joint_fit_neutron_xray_pd_cwl_pbso4() -> None:
     project.analysis.current_calculator = "cryspy"
     project.analysis.current_minimizer = "lmfit (leastsq)"
     project.analysis.fit_mode = 'joint'
-    project.analysis.joint_fit['xrd'] = 0.3
-    project.analysis.joint_fit['npd'] = 0.7
+    project.analysis.joint_fit_experiments['xrd'] = 0.3
+    project.analysis.joint_fit_experiments['npd'] = 0.7
 
     # Define free parameters
     model.cell.length_a.free = True
@@ -97,8 +97,8 @@ def test_joint_fit_neutron_xray_pd_cwl_pbso4() -> None:
     assert_almost_equal(chi_squared, 14.4, decimal=1)
 
     # Results should be different if weights are changed
-    project.analysis.joint_fit['xrd'] = 0.9
-    project.analysis.joint_fit['npd'] = 0.1
+    project.analysis.joint_fit_experiments['xrd'] = 0.9
+    project.analysis.joint_fit_experiments['npd'] = 0.1
 
     project.analysis.fit()
     assert not isclose(chi_squared, 14.4)