diff --git a/.gitignore b/.gitignore
index 50a2aeb0..c7ec6607 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,5 @@
 __pycache__/
 *.py[cod]
 
-src/vesuvio_analysis/core_functions/bootstrap_ws/
 figures/
-tests/analysis/data/inputs/sample_test/output_files/
+tests/**/output_files/
diff --git a/src/mvesuvio/analysis_fitting.py b/src/mvesuvio/analysis_fitting.py
index 55a63b09..2b6c13b0 100644
--- a/src/mvesuvio/analysis_fitting.py
+++ b/src/mvesuvio/analysis_fitting.py
@@ -23,18 +23,15 @@ def fitInYSpaceProcedure(yFitIC, IC, wsTOF):
         print(f"Workspace to fit {wsTOF} not found.")
         return
 
-    ncpForEachMass = extractNCPFromWorkspaces(wsTOF, IC)
     wsResSum, wsRes = calculateMantidResolutionFirstMass(IC, yFitIC, wsTOF)
 
-    wsTOFMass0 = subtractAllMassesExceptFirst(IC, wsTOF, ncpForEachMass)
+    wsTOFMass0 = subtract_profiles_except_lightest(IC, wsTOF)
 
     if yFitIC.subtractFSE:
         wsFSEMass0 = find_ws_name_fse_first_mass(IC)
         wsTOFMass0 = Minus(wsTOFMass0, wsFSEMass0, OutputWorkspace=wsTOFMass0.name() + "_fse")
 
-    wsJoY, wsJoYAvg = ySpaceReduction(
-        wsTOFMass0, IC.masses[0], yFitIC, ncpForEachMass[:, 0, :]
-    )
+    wsJoY, wsJoYAvg = ySpaceReduction(wsTOFMass0, IC.masses[0], yFitIC, IC)
 
     if yFitIC.symmetrisationFlag:
         wsJoYAvg = symmetrizeWs(wsJoYAvg)
@@ -69,34 +66,6 @@ def find_ws_name_fse_first_mass(ic):
     return ws_names_fse[np.argmin(ws_masses)]
 
 
-def extractNCPFromWorkspaces(wsFinal, ic):
-    """Extra function to extract ncps from loaded ws in mantid."""
-
-    for ws_name in mtd.getObjectNames():
-        if ws_name.startswith(ic.name+'_'+str(ic.noOfMSIterations)) and ws_name.endswith('ncp'):
-
-            if 'total' in ws_name:
-                continue
-
-            ws = mtd[ws_name]
-            dataY = ws.extractY()[np.newaxis, :, :]
-            try:
-                ncpForEachMass = np.append(ncpForEachMass, dataY, axis=0)
-            except UnboundLocalError:
-                ncpForEachMass = dataY 
-
-    # Ensure shape of ncp matches data
-    shape = ncpForEachMass.shape
-    assert shape[0] == len(ic.masses)
-    assert shape[1] == wsFinal.getNumberHistograms()
-    # Final dimension can be missing last col or not
-    assert (shape[2] == wsFinal.blocksize()) | (shape[2] == wsFinal.blocksize() - 1)
-
-    ncpForEachMass = switchFirstTwoAxis(ncpForEachMass)  # Organizes ncp by spectra
-    print("\nExtracted NCP profiles from workspaces.\n")
-    return ncpForEachMass
-
-
 def calculateMantidResolutionFirstMass(IC, yFitIC, ws):
     mass = IC.masses[0]
 
@@ -125,36 +94,26 @@ def calculateMantidResolutionFirstMass(IC, yFitIC, ws):
     return wsResSum, mtd[resName]
 
 
-def subtractAllMassesExceptFirst(ic, ws, ncpForEachMass):
+def subtract_profiles_except_lightest(ic, ws):
     """
     Isolates TOF data from first mass only.
     Input: ws containing TOF values, NCP for all mass profiles.
     Output: ws with all profiles except first subtracted.
     """
+    if len(ic.masses) == 1:
+        return
 
-    ncpForEachMass = switchFirstTwoAxis(ncpForEachMass)
-    # Select all masses other than the first one
-    ncpForEachMassExceptFirst = ncpForEachMass[1:, :, :]
-    # Sum the ncpTotal for remaining masses
-    ncpTotalExceptFirst = np.sum(ncpForEachMassExceptFirst, axis=0)
+    ws_name_lightest_mass = ic.name + '_' + str(ic.noOfMSIterations) + '_' + str(min(ic.masses)) + '_ncp'
+    ws_name_profiles = ic.name + '_' + str(ic.noOfMSIterations) + '_total_ncp'
 
-    dataX, dataY, dataE = extractWS(ws)
+    wsNcpExceptFirst = Minus(mtd[ws_name_profiles], mtd[ws_name_lightest_mass], 
+                             OutputWorkspace=ws_name_profiles + '_except_lightest')
 
-    # Adjust for last column missing or not
-    dataY[:, : ncpTotalExceptFirst.shape[1]] -= ncpTotalExceptFirst
+    SumSpectra(wsNcpExceptFirst.name(), OutputWorkspace=wsNcpExceptFirst.name() + "_sum")
 
-    # Ignore any masked bins (columns) from initial ws
-    mask = np.all(ws.extractY() == 0, axis=0)
-    dataY[:, mask] = 0
-
-    wsSubMass = CloneWorkspace(InputWorkspace=ws, OutputWorkspace=ws.name() + "_m0")
-    passDataIntoWS(dataX, dataY, dataE, wsSubMass)
-    wsMask, maskList = ExtractMask(ws)
-    MaskDetectors(Workspace=wsSubMass, MaskedWorkspace=wsMask)
-    SumSpectra(
-        InputWorkspace=wsSubMass.name(), OutputWorkspace=wsSubMass.name() + "_Sum"
-    )
-    return wsSubMass
+    wsFirstMass = Minus(ws, wsNcpExceptFirst, OutputWorkspace=ws.name()+"_m0")
+    SumSpectra(wsFirstMass.name(), OutputWorkspace=wsFirstMass.name() + "_sum")
+    return wsFirstMass
 
 
 def switchFirstTwoAxis(A):
@@ -164,9 +123,12 @@ def switchFirstTwoAxis(A):
     return np.stack(np.split(A, len(A), axis=0), axis=2)[0]
 
 
-def ySpaceReduction(wsTOF, mass0, yFitIC, ncp):
+def ySpaceReduction(wsTOF, mass0, yFitIC, ic):
     """Seperate procedures depending on masking specified."""
 
+    ws_name_lightest_mass = ic.name + '_' + str(ic.noOfMSIterations) + '_' + str(min(ic.masses)) + '_ncp'
+    ncp = mtd[ws_name_lightest_mass].extractY()
+
     rebinPars = yFitIC.rebinParametersForYSpaceFit
 
     if np.any(np.all(wsTOF.extractY() == 0, axis=0)):  # Masked columns present
diff --git a/tests/data/analysis/benchmark/stored_yspace_fit.npz b/tests/data/analysis/benchmark/stored_yspace_fit.npz
deleted file mode 100644
index 88d5012f..00000000
Binary files a/tests/data/analysis/benchmark/stored_yspace_fit.npz and /dev/null differ
diff --git a/tests/data/analysis/benchmark/stored_yspace_fit_GC.npz b/tests/data/analysis/benchmark/stored_yspace_fit_GC.npz
deleted file mode 100644
index aacc2a9e..00000000
Binary files a/tests/data/analysis/benchmark/stored_yspace_fit_GC.npz and /dev/null differ
diff --git a/tests/data/analysis/benchmark/yspace_gauss_test.npz b/tests/data/analysis/benchmark/yspace_gauss_test.npz
new file mode 100644
index 00000000..9956148c
Binary files /dev/null and b/tests/data/analysis/benchmark/yspace_gauss_test.npz differ
diff --git a/tests/data/analysis/benchmark/yspace_gc_test.npz b/tests/data/analysis/benchmark/yspace_gc_test.npz
new file mode 100644
index 00000000..0326d109
Binary files /dev/null and b/tests/data/analysis/benchmark/yspace_gc_test.npz differ
diff --git a/tests/data/analysis/inputs/analysis_test.py b/tests/data/analysis/inputs/analysis_test.py
index 2ae8121c..46975a20 100644
--- a/tests/data/analysis/inputs/analysis_test.py
+++ b/tests/data/analysis/inputs/analysis_test.py
@@ -94,3 +94,10 @@ class YSpaceFitInputs:
     globalFit = None
     nGlobalFitGroups = 4
     maskTypeProcedure = None
+
+
+if (__name__ == "__main__") or (__name__ == "mantidqt.widgets.codeeditor.execution"):
+    import mvesuvio
+    from pathlib import Path
+    mvesuvio.set_config(inputs_file=Path(__file__))
+    mvesuvio.run()
diff --git a/tests/data/analysis/inputs/wsFinal_ncp_0.nxs b/tests/data/analysis/inputs/wsFinal_ncp_0.nxs
deleted file mode 100644
index 0b0c81dd..00000000
Binary files a/tests/data/analysis/inputs/wsFinal_ncp_0.nxs and /dev/null differ
diff --git a/tests/data/analysis/inputs/wsFinal_ncp_1.nxs b/tests/data/analysis/inputs/wsFinal_ncp_1.nxs
deleted file mode 100644
index 6811809f..00000000
Binary files a/tests/data/analysis/inputs/wsFinal_ncp_1.nxs and /dev/null differ
diff --git a/tests/data/analysis/inputs/wsFinal_ncp_2.nxs b/tests/data/analysis/inputs/wsFinal_ncp_2.nxs
deleted file mode 100644
index 52ec0350..00000000
Binary files a/tests/data/analysis/inputs/wsFinal_ncp_2.nxs and /dev/null differ
diff --git a/tests/data/analysis/inputs/wsFinal_ncp_3.nxs b/tests/data/analysis/inputs/wsFinal_ncp_3.nxs
deleted file mode 100644
index e2e57482..00000000
Binary files a/tests/data/analysis/inputs/wsFinal_ncp_3.nxs and /dev/null differ
diff --git a/tests/data/analysis/inputs/wsFinal_ncp_sum.nxs b/tests/data/analysis/inputs/wsFinal_ncp_sum.nxs
deleted file mode 100644
index 5792b09f..00000000
Binary files a/tests/data/analysis/inputs/wsFinal_ncp_sum.nxs and /dev/null differ
diff --git a/tests/data/analysis/inputs/yspace_gauss_test.py b/tests/data/analysis/inputs/yspace_gauss_test.py
index b3c57316..efe7c7ae 100644
--- a/tests/data/analysis/inputs/yspace_gauss_test.py
+++ b/tests/data/analysis/inputs/yspace_gauss_test.py
@@ -6,8 +6,15 @@
 ForwardAnalysisInputs.noOfMSIterations = 1
 ForwardAnalysisInputs.firstSpec = 164
 ForwardAnalysisInputs.lastSpec = 175
+ForwardAnalysisInputs.maskedSpecAllNo = [173, 174]
 ForwardAnalysisInputs.fit_in_y_space = True 
 BackwardAnalysisInputs.fit_in_y_space = False
 ForwardAnalysisInputs.run_this_scattering_type = True 
 BackwardAnalysisInputs.run_this_scattering_type = False
 YSpaceFitInputs.fitModel = "SINGLE_GAUSSIAN"
+
+if (__name__ == "__main__") or (__name__ == "mantidqt.widgets.codeeditor.execution"):
+    import mvesuvio
+    from pathlib import Path
+    mvesuvio.set_config(inputs_file=Path(__file__))
+    mvesuvio.run()
diff --git a/tests/data/analysis/inputs/yspace_gauss_test/output_files/spec_164-175_iter_1_GC_MS.npz_ySpaceFit.npz b/tests/data/analysis/inputs/yspace_gauss_test/output_files/spec_164-175_iter_1_GC_MS.npz_ySpaceFit.npz
deleted file mode 100644
index 1483d99b..00000000
Binary files a/tests/data/analysis/inputs/yspace_gauss_test/output_files/spec_164-175_iter_1_GC_MS.npz_ySpaceFit.npz and /dev/null differ
diff --git a/tests/data/analysis/inputs/yspace_gc_test.py b/tests/data/analysis/inputs/yspace_gc_test.py
index 05a87a6f..cbd11323 100644
--- a/tests/data/analysis/inputs/yspace_gc_test.py
+++ b/tests/data/analysis/inputs/yspace_gc_test.py
@@ -7,9 +7,17 @@
 ForwardAnalysisInputs.noOfMSIterations = 1
 ForwardAnalysisInputs.firstSpec = 164
 ForwardAnalysisInputs.lastSpec = 175
+ForwardAnalysisInputs.maskedSpecAllNo = [173, 174]
 ForwardAnalysisInputs.fit_in_y_space = True 
 BackwardAnalysisInputs.fit_in_y_space = False
 ForwardAnalysisInputs.run_this_scattering_type = True 
 BackwardAnalysisInputs.run_this_scattering_type = False
 YSpaceFitInputs.fitModel = "GC_C4_C6"
 YSpaceFitInputs.symmetrisationFlag = False 
+
+
+if (__name__ == "__main__") or (__name__ == "mantidqt.widgets.codeeditor.execution"):
+    import mvesuvio
+    from pathlib import Path
+    mvesuvio.set_config(inputs_file=Path(__file__))
+    mvesuvio.run()
diff --git a/tests/data/analysis/inputs/yspace_gc_test/output_files/spec_164-175_iter_1_GC_MS.npz_ySpaceFit.npz b/tests/data/analysis/inputs/yspace_gc_test/output_files/spec_164-175_iter_1_GC_MS.npz_ySpaceFit.npz
deleted file mode 100644
index 7f87172a..00000000
Binary files a/tests/data/analysis/inputs/yspace_gc_test/output_files/spec_164-175_iter_1_GC_MS.npz_ySpaceFit.npz and /dev/null differ
diff --git a/tests/data/analysis/inputs/wsFinal.nxs b/tests/data/analysis/inputs/yspace_tests_fwd_1.nxs
similarity index 59%
rename from tests/data/analysis/inputs/wsFinal.nxs
rename to tests/data/analysis/inputs/yspace_tests_fwd_1.nxs
index a6990266..ca32a93c 100644
Binary files a/tests/data/analysis/inputs/wsFinal.nxs and b/tests/data/analysis/inputs/yspace_tests_fwd_1.nxs differ
diff --git a/tests/data/analysis/inputs/yspace_tests_fwd_1_1.0079_ncp.nxs b/tests/data/analysis/inputs/yspace_tests_fwd_1_1.0079_ncp.nxs
new file mode 100644
index 00000000..c8319e56
Binary files /dev/null and b/tests/data/analysis/inputs/yspace_tests_fwd_1_1.0079_ncp.nxs differ
diff --git a/tests/data/analysis/inputs/yspace_tests_fwd_1_total_ncp.nxs b/tests/data/analysis/inputs/yspace_tests_fwd_1_total_ncp.nxs
new file mode 100644
index 00000000..197c80aa
Binary files /dev/null and b/tests/data/analysis/inputs/yspace_tests_fwd_1_total_ncp.nxs differ
diff --git a/tests/system/analysis/test_yspace_fit.py b/tests/system/analysis/test_yspace_fit.py
index 71c34f84..7dd4f124 100644
--- a/tests/system/analysis/test_yspace_fit.py
+++ b/tests/system/analysis/test_yspace_fit.py
@@ -1,5 +1,5 @@
 from mvesuvio.main.run_routine import Runner 
-from mantid.simpleapi import Load
+from mantid.simpleapi import Load, Plus, mtd, CreateWorkspace, CloneWorkspace
 from mantid.api import AnalysisDataService
 from pathlib import Path
 import numpy as np
@@ -43,17 +43,19 @@ def get_current_result(cls):
     @classmethod
     def _load_workspaces(cls):
         AnalysisDataService.clear()
-        scriptName = handle_config.get_script_name()
-        wsFinal = Load(
-            str(cls._input_data_path / "wsFinal.nxs"),
-            OutputWorkspace=scriptName + "_fwd_1",
+        Load(
+            str(cls._input_data_path / "yspace_tests_fwd_1.nxs"),
+            OutputWorkspace="yspace_gauss_test_fwd_1"
         )
-        for i in range(4):
-            fileName = "wsFinal_ncp_" + str(i) + ".nxs"
-            Load(
-                str(cls._input_data_path / fileName),
-                OutputWorkspace=wsFinal.name() + "_label" + str(i) +"_ncp",
-            )
+        Load(
+            str(cls._input_data_path / "yspace_tests_fwd_1_total_ncp.nxs"),
+            OutputWorkspace="yspace_gauss_test_fwd_1_total_ncp"
+        )
+        Load(
+            str(cls._input_data_path / "yspace_tests_fwd_1_1.0079_ncp.nxs"),
+            OutputWorkspace="yspace_gauss_test_fwd_1_1.0079_ncp"
+        )
+        return
 
     @classmethod
     def _run(cls):
@@ -63,7 +65,7 @@ def _run(cls):
 
     @classmethod
     def _load_benchmark_results(cls):
-        cls._benchmarkResults = np.load(str(cls._benchmark_path / "stored_yspace_fit.npz"))
+        cls._benchmarkResults = np.load(str(cls._benchmark_path / "yspace_gauss_test.npz"))
 
 
 class TestSymSumYSpace(unittest.TestCase):
diff --git a/tests/system/analysis/test_yspace_fit_GC.py b/tests/system/analysis/test_yspace_fit_GC.py
index 44788202..534ab767 100644
--- a/tests/system/analysis/test_yspace_fit_GC.py
+++ b/tests/system/analysis/test_yspace_fit_GC.py
@@ -43,17 +43,19 @@ def get_current_result(cls):
     @classmethod
     def _load_workspaces(cls):
         AnalysisDataService.clear()
-        scriptName = handle_config.get_script_name()
-        wsFinal = Load(
-            str(cls._input_data_path / "wsFinal.nxs"),
-            OutputWorkspace=scriptName + "_fwd_1",
+        Load(
+            str(cls._input_data_path / "yspace_tests_fwd_1.nxs"),
+            OutputWorkspace="yspace_gc_test_fwd_1"
         )
-        for i in range(4):
-            fileName = "wsFinal_ncp_" + str(i) + ".nxs"
-            Load(
-                str(cls._input_data_path / fileName),
-                OutputWorkspace=wsFinal.name() + "_label" + str(i) +"_ncp",
-            )
+        Load(
+            str(cls._input_data_path / "yspace_tests_fwd_1_total_ncp.nxs"),
+            OutputWorkspace="yspace_gc_test_fwd_1_total_ncp"
+        )
+        Load(
+            str(cls._input_data_path / "yspace_tests_fwd_1_1.0079_ncp.nxs"),
+            OutputWorkspace="yspace_gc_test_fwd_1_1.0079_ncp"
+        )
+        return
 
     @classmethod
     def _run(cls):
@@ -64,7 +66,7 @@ def _run(cls):
     @classmethod
     def _load_benchmark_results(cls):
         cls._benchmarkResults = np.load(
-            str(cls._benchmark_path / "stored_yspace_fit_GC.npz")
+            str(cls._benchmark_path / "yspace_gc_test.npz")
         )