From 358c0d615b95adcddcb3eea67aa6df6acb21cbf2 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Thu, 1 Dec 2022 16:20:29 -0600
Subject: [PATCH 01/24] add extract_utils.py for EXTRACT

---
 element_interface/extract_utils.py | 84 ++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 element_interface/extract_utils.py

diff --git a/element_interface/extract_utils.py b/element_interface/extract_utils.py
new file mode 100644
index 0000000..55204ed
--- /dev/null
+++ b/element_interface/extract_utils.py
@@ -0,0 +1,84 @@
+import os
+from pathlib import Path
+from datetime import datetime
+
+
+class EXTRACT:
+    m_template = r"""
+% Load Data
+data = load('{scanfile}');
+M = data.M;
+
+% Input Paramaters
+config = struct();
+{parameters_list_string}
+
+% Perform Extraction
+output = extractor(M, config);
+write({output_fullpath})
+"""
+
+    def __init__(self, scanfile_fullpath, parameters, output_dir) -> None:
+        assert isinstance(self.parameters, dict)
+
+        self.scanfile = Path(scanfile_fullpath)
+        self.output_dir = Path(output_dir)
+        self.parameters = parameters
+
+    def write_matlab_run_script(self):
+        """Compose the matlab script, run_extract.m, that would run the EXTRACT trigger."""
+
+        assert self.scanfile.exists()
+
+        self.output_fullpath = (
+            Path(self.output_dir) / f"{self.scanfile.stem}_extract_output.mat",
+        )
+
+        m_file_content = self.m_template.format(
+            **dict(
+                parameters_list_string="\n".join(
+                    [
+                        f"config.{k} = '{v}';"
+                        if isinstance(v, str)
+                        else f"config.{k} = {str(v).lower()};"
+                        if isinstance(v, bool)
+                        else f"config.{k} = {v};"
+                        for k, v in self.parameters.items()
+                    ]
+                ),
+                scanfile=self.scanfile,
+                output_fullpath=self.output_fullpath,
+            )
+        )
+
+        self.m_file_fp = self.output_dir / "run_extract.m"
+
+        with open(self.m_file_fp, "w") as f:
+            f.write(m_file_content)
+
+    def run(self):
+        """Run run_extract.m script."""
+
+        current_dir = Path.cwd()
+        os.chdir(self.output_dir)
+
+        run_status = {"execution_time": datetime.utcnow()}
+        try:
+            import matlab.engine
+
+            eng = matlab.engine.start_matlab()
+            eng.run_extract()
+        except Exception as e:
+            raise e
+        finally:
+            os.chdir(current_dir)
+
+        run_status["execution_duration"] = (
+            datetime.utcnow() - run_status["execution_time"]
+        ).total_seconds()
+        return run_status
+
+    def load_results(self):
+        from scipy.io import loadmat
+
+        self.results = loadmat(self.output_fullpath)

From 87afa22e9fc617c58dbce68d5ef780fd2e9dbdc9 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Thu, 1 Dec 2022 16:35:54 -0600
Subject: [PATCH 02/24] add docstring

---
 element_interface/extract_utils.py | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/element_interface/extract_utils.py b/element_interface/extract_utils.py
index 55204ed..3130b4a 100644
--- a/element_interface/extract_utils.py
+++ b/element_interface/extract_utils.py
@@ -1,4 +1,5 @@
 import os
+from typing import Union
 from pathlib import Path
 from datetime import datetime
 
@@ -18,7 +19,19 @@ class EXTRACT:
 write({output_fullpath})
 """
 
-    def __init__(self, scanfile_fullpath, parameters, output_dir) -> None:
+    def __init__(
+        self,
+        scanfile_fullpath: Union[str, Path],
+        parameters: dict,
+        output_dir: Union[str, Path],
+    ) -> None:
+        """A helper class to trigger EXTRACT analysis as well as to load its results.
+
+        Args:
+            scanfile_fullpath (Union[str, Path]): Full path of the scan
+            parameters (dict): EXTRACT input paramaters.
+            output_dir (Union[str, Path]): Directory to store the outputs of EXTRACT analysis.
+        """
         assert isinstance(self.parameters, dict)
 
         self.scanfile = Path(scanfile_fullpath)
@@ -26,7 +39,9 @@ def __init__(self, scanfile_fullpath, parameters, output_dir) -> None:
         self.parameters = parameters
 
     def write_matlab_run_script(self):
-        """Compose the matlab script, run_extract.m, that would run the EXTRACT trigger."""
+        """Compose a matlab script and save in the run_extract.m file.
+
+        The composed script is basically the formatted version of the m_template attrribute."""
 
         assert self.scanfile.exists()
 
@@ -79,6 +94,7 @@ def run(self):
         return run_status
 
     def load_results(self):
+        """Load the EXTRACT results"""
         from scipy.io import loadmat
 
         self.results = loadmat(self.output_fullpath)

From 99c4fb874e49ddcd736bffaa61005a73e98add13 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Fri, 2 Dec 2022 09:20:22 -0600
Subject: [PATCH 03/24] fix ugly template style

---
 element_interface/extract_utils.py | 35 ++++++++++++++++--------------
 1 file changed, 19 insertions(+), 16 deletions(-)

diff --git a/element_interface/extract_utils.py b/element_interface/extract_utils.py
index 3130b4a..d730e70 100644
--- a/element_interface/extract_utils.py
+++ b/element_interface/extract_utils.py
@@ -2,22 +2,25 @@
 from typing import Union
 from pathlib import Path
 from datetime import datetime
+from textwrap import dedent
 
 
 class EXTRACT:
-    m_template = r"""
-% Load Data
-data = load('{scanfile}');
-M = data.M;
-
-% Input Paramaters
-config = struct();
-{parameters_list_string}
-
-% Perform Extraction
-output = extractor(M, config);
-write({output_fullpath})
-"""
+    m_template = dedent(
+        """
+        % Load Data
+        data = load('{scanfile}');
+        M = data.M;
+        
+        % Input Paramaters
+        config = struct();
+        {parameters_list_string}
+        
+        % Perform Extraction
+        output = extractor(M, config);
+        write({output_fullpath})
+        """
+    )
 
     def __init__(
         self,
@@ -32,7 +35,7 @@ def __init__(
             parameters (dict): EXTRACT input paramaters.
             output_dir (Union[str, Path]): Directory to store the outputs of EXTRACT analysis.
         """
-        assert isinstance(self.parameters, dict)
+        assert isinstance(parameters, dict)
 
         self.scanfile = Path(scanfile_fullpath)
         self.output_dir = Path(output_dir)
@@ -43,7 +46,7 @@ def write_matlab_run_script(self):
 
         The composed script is basically the formatted version of the m_template attrribute."""
 
-        assert self.scanfile.exists()
+        # assert self.scanfile.exists()
 
         self.output_fullpath = (
             Path(self.output_dir) / f"{self.scanfile.stem}_extract_output.mat",
@@ -64,7 +67,7 @@ def write_matlab_run_script(self):
                 scanfile=self.scanfile,
                 output_fullpath=self.output_fullpath,
             )
-        )
+        ).lstrip()
 
         self.m_file_fp = self.output_dir / "run_extract.m"
 

From 4fd50a7922f588c9a62eefa422a375e02c0a500e Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Tue, 13 Dec 2022 10:39:54 -0600
Subject: [PATCH 04/24] remove return run_status

---
 element_interface/extract_utils.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/element_interface/extract_utils.py b/element_interface/extract_utils.py
index d730e70..d946d9a 100644
--- a/element_interface/extract_utils.py
+++ b/element_interface/extract_utils.py
@@ -18,7 +18,7 @@ class EXTRACT:
         
         % Perform Extraction
         output = extractor(M, config);
-        write({output_fullpath})
+        write({output_fullpath});
         """
     )
 
@@ -28,7 +28,7 @@ def __init__(
         parameters: dict,
         output_dir: Union[str, Path],
     ) -> None:
-        """A helper class to trigger EXTRACT analysis as well as to load its results.
+        """A helper class to trigger EXTRACT analysis in element-calcium-imaging.
 
         Args:
             scanfile_fullpath (Union[str, Path]): Full path of the scan
@@ -65,7 +65,7 @@ def write_matlab_run_script(self):
                     ]
                 ),
                 scanfile=self.scanfile,
-                output_fullpath=self.output_fullpath,
+                output_fullpath=self.output_fullpath.as_posix(),
             )
         ).lstrip()
 
@@ -77,10 +77,12 @@ def write_matlab_run_script(self):
     def run(self):
         """Run run_extract.m script."""
 
+        self.write_matlab_run_script()
+
         current_dir = Path.cwd()
         os.chdir(self.output_dir)
 
-        run_status = {"execution_time": datetime.utcnow()}
+        run_status = {"processing_time": datetime.utcnow()}
         try:
             import matlab.engine
 
@@ -92,9 +94,8 @@ def run(self):
             os.chdir(current_dir)
 
         run_status["execution_duration"] = (
-            datetime.utcnow() - run_status["execution_time"]
+            datetime.utcnow() - run_status["processing_time"]
         ).total_seconds()
-        return run_status
 
     def load_results(self):
         """Load the EXTRACT results"""

From 6ebf019b58c182ef6ba63edda1ffd048b3762129 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Tue, 13 Dec 2022 13:36:19 -0600
Subject: [PATCH 05/24] switch from write to save

---
 element_interface/extract_utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/element_interface/extract_utils.py b/element_interface/extract_utils.py
index d946d9a..13e8873 100644
--- a/element_interface/extract_utils.py
+++ b/element_interface/extract_utils.py
@@ -18,7 +18,7 @@ class EXTRACT:
         
         % Perform Extraction
         output = extractor(M, config);
-        write({output_fullpath});
+        save('{output_fullpath}', 'output');
         """
     )
 
@@ -49,7 +49,7 @@ def write_matlab_run_script(self):
         # assert self.scanfile.exists()
 
         self.output_fullpath = (
-            Path(self.output_dir) / f"{self.scanfile.stem}_extract_output.mat",
+            self.output_dir / f"{self.scanfile.stem}_extract_output.mat"
         )
 
         m_file_content = self.m_template.format(

From 04b8f69cda177006bf84eed580366580da9c2b63 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Tue, 13 Dec 2022 18:49:23 -0600
Subject: [PATCH 06/24] add loader and trigger

---
 element_interface/extract_loader.py           | 51 +++++++++++++++++++
 .../{extract_utils.py => extract_trigger.py}  | 18 ++-----
 2 files changed, 56 insertions(+), 13 deletions(-)
 create mode 100644 element_interface/extract_loader.py
 rename element_interface/{extract_utils.py => extract_trigger.py} (88%)

diff --git a/element_interface/extract_loader.py b/element_interface/extract_loader.py
new file mode 100644
index 0000000..0bb6f0a
--- /dev/null
+++ b/element_interface/extract_loader.py
@@ -0,0 +1,51 @@
+import numpy as np
+from pathlib import Path
+
+
+class EXTRACT_loader:
+    def __init__(self, extract_dir: str):
+        """Initialize EXTRACT loader class
+
+        Args:
+            extract_dir (str): string, absolute file path to Extract directory
+
+        Raises:
+            FileNotFoundError: Could not find EXTRACT results
+        """
+        from scipy.io import loadmat
+
+        output_file = list(Path(extract_dir).glob("*_extract_output.mat"))
+
+        if not output_file:
+            raise FileNotFoundError(
+                "EXTRACT output result files not found at {}".format(extract_dir)
+            )
+
+        results = loadmat(output_file[0])
+        self.S = results["output"][0]["spatial_weights"][0]  # (Height, Width, Time)
+        self.T = results["output"][0]["temporal_weights"][0]  # (Time, MaskId)
+
+    def load_results(self):
+        """Load the EXTRACT results"""
+        from scipy.sparse import find
+
+        S_tr = self.S.transpose([2, 0, 1])  # Mask_no, Height, Width
+
+        masks = []
+
+        for mask_id, s in enumerate(S_tr):
+            ypixels, xpixels, weights = find(s)
+            masks.append(
+                dict(
+                    mask_id=mask_id,
+                    mask_npix=len(weights),
+                    mask_weights=weights,
+                    mask_center_x=int(np.average(xpixels, weights=weights) + 0.5),
+                    mask_center_y=int(np.average(ypixels, weights=weights) + 0.5),
+                    mask_center_z=None,
+                    mask_xpix=xpixels,
+                    mask_ypix=ypixels,
+                    mask_zpix=None,
+                )
+            )
+        return masks
diff --git a/element_interface/extract_utils.py b/element_interface/extract_trigger.py
similarity index 88%
rename from element_interface/extract_utils.py
rename to element_interface/extract_trigger.py
index 13e8873..885e306 100644
--- a/element_interface/extract_utils.py
+++ b/element_interface/extract_trigger.py
@@ -1,11 +1,11 @@
 import os
 from typing import Union
 from pathlib import Path
-from datetime import datetime
 from textwrap import dedent
+from datetime import datetime
 
 
-class EXTRACT:
+class EXTRACT_trigger:
     m_template = dedent(
         """
         % Load Data
@@ -42,11 +42,9 @@ def __init__(
         self.parameters = parameters
 
     def write_matlab_run_script(self):
-        """Compose a matlab script and save in the run_extract.m file.
-
-        The composed script is basically the formatted version of the m_template attrribute."""
+        """Compose a matlab script and save it with the name run_extract.m.
 
-        # assert self.scanfile.exists()
+        The composed script is basically the formatted version of the m_template attribute."""
 
         self.output_fullpath = (
             self.output_dir / f"{self.scanfile.stem}_extract_output.mat"
@@ -75,7 +73,7 @@ def write_matlab_run_script(self):
             f.write(m_file_content)
 
     def run(self):
-        """Run run_extract.m script."""
+        """Run the matlab run_extract.m script."""
 
         self.write_matlab_run_script()
 
@@ -96,9 +94,3 @@ def run(self):
         run_status["execution_duration"] = (
             datetime.utcnow() - run_status["processing_time"]
         ).total_seconds()
-
-    def load_results(self):
-        """Load the EXTRACT results"""
-        from scipy.io import loadmat
-
-        self.results = loadmat(self.output_fullpath)

From e8d5b0a84c0dab7f77e02c619e54e4f9667877e3 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Tue, 13 Dec 2022 18:53:22 -0600
Subject: [PATCH 07/24] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 20335e9..fd9822f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 
 + Add - mkdocs documentation
 + Add - improved docstrings for mkdocs
++ Add - EXTRACT trigger and loader tools
 
 ## [0.3.0] - 2022-10-7
 

From 7cffc25dbfa87fbd869025b432cade1c07a70af0 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Tue, 13 Dec 2022 19:12:07 -0600
Subject: [PATCH 08/24] add creation_time

---
 element_interface/extract_loader.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/element_interface/extract_loader.py b/element_interface/extract_loader.py
index 0bb6f0a..ca5ca77 100644
--- a/element_interface/extract_loader.py
+++ b/element_interface/extract_loader.py
@@ -1,5 +1,6 @@
 import numpy as np
 from pathlib import Path
+from datetime import datetime
 
 
 class EXTRACT_loader:
@@ -22,6 +23,8 @@ def __init__(self, extract_dir: str):
             )
 
         results = loadmat(output_file[0])
+
+        self.creation_time = datetime.utcnow()
         self.S = results["output"][0]["spatial_weights"][0]  # (Height, Width, Time)
         self.T = results["output"][0]["temporal_weights"][0]  # (Time, MaskId)
 

From d2eb1e82d2da9ddfeed6f401a9cfb9f0c0bbad13 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 11:54:39 -0600
Subject: [PATCH 09/24] Update element_interface/extract_loader.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_loader.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/element_interface/extract_loader.py b/element_interface/extract_loader.py
index ca5ca77..2b0a0e1 100644
--- a/element_interface/extract_loader.py
+++ b/element_interface/extract_loader.py
@@ -8,7 +8,7 @@ def __init__(self, extract_dir: str):
         """Initialize EXTRACT loader class
 
         Args:
-            extract_dir (str): string, absolute file path to Extract directory
+            extract_dir (str): string, absolute file path to EXTRACT directory
 
         Raises:
             FileNotFoundError: Could not find EXTRACT results

From 2ab366daa1b6e66df67490e7c4371542c3986a74 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 14:17:49 -0600
Subject: [PATCH 10/24] Update element_interface/extract_loader.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_loader.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/element_interface/extract_loader.py b/element_interface/extract_loader.py
index 2b0a0e1..93f6381 100644
--- a/element_interface/extract_loader.py
+++ b/element_interface/extract_loader.py
@@ -25,7 +25,7 @@ def __init__(self, extract_dir: str):
         results = loadmat(output_file[0])
 
         self.creation_time = datetime.utcnow()
-        self.S = results["output"][0]["spatial_weights"][0]  # (Height, Width, Time)
+        self.S = results["output"][0]["spatial_weights"][0]  # (Height, Width, MaskId)
         self.T = results["output"][0]["temporal_weights"][0]  # (Time, MaskId)
 
     def load_results(self):

From e3ff2adf5ba33854394848aea79a8308467574f0 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 14:18:10 -0600
Subject: [PATCH 11/24] Update element_interface/extract_loader.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_loader.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/element_interface/extract_loader.py b/element_interface/extract_loader.py
index 93f6381..23b5c3e 100644
--- a/element_interface/extract_loader.py
+++ b/element_interface/extract_loader.py
@@ -29,7 +29,11 @@ def __init__(self, extract_dir: str):
         self.T = results["output"][0]["temporal_weights"][0]  # (Time, MaskId)
 
     def load_results(self):
-        """Load the EXTRACT results"""
+        """Load the EXTRACT results
+        
+        Returns:
+            masks (dict): Details of the masks identified with the EXTRACT segmentation package.
+        """
         from scipy.sparse import find
 
         S_tr = self.S.transpose([2, 0, 1])  # Mask_no, Height, Width

From c18aa11adf37547cac446e899901f961dd206492 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 14:18:35 -0600
Subject: [PATCH 12/24] Update element_interface/extract_loader.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_loader.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/element_interface/extract_loader.py b/element_interface/extract_loader.py
index 23b5c3e..ac5aa0b 100644
--- a/element_interface/extract_loader.py
+++ b/element_interface/extract_loader.py
@@ -36,7 +36,7 @@ def load_results(self):
         """
         from scipy.sparse import find
 
-        S_tr = self.S.transpose([2, 0, 1])  # Mask_no, Height, Width
+        S_transposed = self.S.transpose([2, 0, 1])  # MaskId, Height, Width
 
         masks = []
 

From e5ed418cec7df05a4c2998615ea2e445b5f41751 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 14:18:55 -0600
Subject: [PATCH 13/24] Update element_interface/extract_trigger.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_trigger.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/element_interface/extract_trigger.py b/element_interface/extract_trigger.py
index 885e306..01a78fc 100644
--- a/element_interface/extract_trigger.py
+++ b/element_interface/extract_trigger.py
@@ -31,7 +31,7 @@ def __init__(
         """A helper class to trigger EXTRACT analysis in element-calcium-imaging.
 
         Args:
-            scanfile_fullpath (Union[str, Path]): Full path of the scan
+            scanfile (Union[str, Path]): Full path of the scan
             parameters (dict): EXTRACT input paramaters.
             output_dir (Union[str, Path]): Directory to store the outputs of EXTRACT analysis.
         """

From d93c2de8e85356322356e7e5954e00475c4b743b Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 14:19:03 -0600
Subject: [PATCH 14/24] Update element_interface/extract_loader.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_loader.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/element_interface/extract_loader.py b/element_interface/extract_loader.py
index ac5aa0b..7bc6c8e 100644
--- a/element_interface/extract_loader.py
+++ b/element_interface/extract_loader.py
@@ -40,7 +40,7 @@ def load_results(self):
 
         masks = []
 
-        for mask_id, s in enumerate(S_tr):
+        for mask_id, s in enumerate(S_transposed):
             ypixels, xpixels, weights = find(s)
             masks.append(
                 dict(

From 3517d139c53b817b74d52f70dbb2e8da49f645cc Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 14:19:11 -0600
Subject: [PATCH 15/24] Update element_interface/extract_loader.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_loader.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/element_interface/extract_loader.py b/element_interface/extract_loader.py
index 7bc6c8e..3985198 100644
--- a/element_interface/extract_loader.py
+++ b/element_interface/extract_loader.py
@@ -1,3 +1,4 @@
+import os
 import numpy as np
 from pathlib import Path
 from datetime import datetime

From 1796c521275819d19535ddd6ed1c71a63173c9c3 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 14:19:36 -0600
Subject: [PATCH 16/24] Update element_interface/extract_trigger.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_trigger.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/element_interface/extract_trigger.py b/element_interface/extract_trigger.py
index 01a78fc..5aeaf97 100644
--- a/element_interface/extract_trigger.py
+++ b/element_interface/extract_trigger.py
@@ -24,7 +24,7 @@ class EXTRACT_trigger:
 
     def __init__(
         self,
-        scanfile_fullpath: Union[str, Path],
+        scanfile: Union[str, Path],
         parameters: dict,
         output_dir: Union[str, Path],
     ) -> None:

From 8554cc31a77093dcd8b2488dbc4c85c0bbf82080 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 14:19:48 -0600
Subject: [PATCH 17/24] Update element_interface/extract_trigger.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_trigger.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/element_interface/extract_trigger.py b/element_interface/extract_trigger.py
index 5aeaf97..2561926 100644
--- a/element_interface/extract_trigger.py
+++ b/element_interface/extract_trigger.py
@@ -37,7 +37,7 @@ def __init__(
         """
         assert isinstance(parameters, dict)
 
-        self.scanfile = Path(scanfile_fullpath)
+        self.scanfile = Path(scanfile)
         self.output_dir = Path(output_dir)
         self.parameters = parameters
 

From bca1a5a8f8a0efafc8367fc6f8f3d982ed4d170d Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 14:29:51 -0600
Subject: [PATCH 18/24] Update element_interface/extract_trigger.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_trigger.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/element_interface/extract_trigger.py b/element_interface/extract_trigger.py
index 2561926..8e9a5ab 100644
--- a/element_interface/extract_trigger.py
+++ b/element_interface/extract_trigger.py
@@ -80,7 +80,6 @@ def run(self):
         current_dir = Path.cwd()
         os.chdir(self.output_dir)
 
-        run_status = {"processing_time": datetime.utcnow()}
         try:
             import matlab.engine
 

From f25669ef7e3944a72886761cd6cd2ce58b6e3e0f Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 14:40:45 -0600
Subject: [PATCH 19/24] Update element_interface/extract_loader.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_loader.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/element_interface/extract_loader.py b/element_interface/extract_loader.py
index 3985198..85f6f00 100644
--- a/element_interface/extract_loader.py
+++ b/element_interface/extract_loader.py
@@ -16,14 +16,14 @@ def __init__(self, extract_dir: str):
         """
         from scipy.io import loadmat
 
-        output_file = list(Path(extract_dir).glob("*_extract_output.mat"))
-
-        if not output_file:
+        try:
+            extract_file = next(Path(extract_dir).glob("*_extract_output.mat"))
+        except StopInteration:
             raise FileNotFoundError(
-                "EXTRACT output result files not found at {}".format(extract_dir)
+                f"EXTRACT output result file is not found at {extract_dir}."
             )
 
-        results = loadmat(output_file[0])
+        results = loadmat(extract_file)
 
         self.creation_time = datetime.utcnow()
         self.S = results["output"][0]["spatial_weights"][0]  # (Height, Width, MaskId)

From caa89c857d5f40c3b5bf51f5db000035238f2333 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 14:41:46 -0600
Subject: [PATCH 20/24] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fd9822f..83f13a3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,6 +37,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 
 + Add - Readers for: `ScanImage`, `Suite2p`, `CaImAn`.
 
+[0.3.1]: https://github.com/datajoint/element-interface/releases/tag/0.3.1
 [0.3.0]: https://github.com/datajoint/element-interface/releases/tag/0.3.0
 [0.2.1]: https://github.com/datajoint/element-interface/releases/tag/0.2.1
 [0.2.0]: https://github.com/datajoint/element-interface/releases/tag/0.2.0

From bb1f15f2dc5c650c59be40a957e250d2e6ffe511 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 15:05:44 -0600
Subject: [PATCH 21/24] Update element_interface/extract_trigger.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_trigger.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/element_interface/extract_trigger.py b/element_interface/extract_trigger.py
index 8e9a5ab..df9d84a 100644
--- a/element_interface/extract_trigger.py
+++ b/element_interface/extract_trigger.py
@@ -16,7 +16,7 @@ class EXTRACT_trigger:
         config = struct();
         {parameters_list_string}
         
-        % Perform Extraction
+        % Run EXTRACT
         output = extractor(M, config);
         save('{output_fullpath}', 'output');
         """

From 1bf75cc9513c57c56945ecf5e6c411b680dc40e0 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 15:06:02 -0600
Subject: [PATCH 22/24] Update element_interface/extract_trigger.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_trigger.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/element_interface/extract_trigger.py b/element_interface/extract_trigger.py
index df9d84a..94db2e8 100644
--- a/element_interface/extract_trigger.py
+++ b/element_interface/extract_trigger.py
@@ -89,7 +89,3 @@ def run(self):
             raise e
         finally:
             os.chdir(current_dir)
-
-        run_status["execution_duration"] = (
-            datetime.utcnow() - run_status["processing_time"]
-        ).total_seconds()

From 0b5dc06e2ff78b72d93ea5d9dab19c184723ca96 Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 15:08:20 -0600
Subject: [PATCH 23/24] Update element_interface/extract_loader.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
---
 element_interface/extract_loader.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/element_interface/extract_loader.py b/element_interface/extract_loader.py
index 85f6f00..ca31949 100644
--- a/element_interface/extract_loader.py
+++ b/element_interface/extract_loader.py
@@ -25,7 +25,7 @@ def __init__(self, extract_dir: str):
 
         results = loadmat(extract_file)
 
-        self.creation_time = datetime.utcnow()
+        self.creation_time = datetime.fromtimestamp(os.stat(extract_file).st_ctime)
         self.S = results["output"][0]["spatial_weights"][0]  # (Height, Width, MaskId)
         self.T = results["output"][0]["temporal_weights"][0]  # (Time, MaskId)
 

From e03c967db7ec80dc0391dfd654b92d7772ad1fca Mon Sep 17 00:00:00 2001
From: Tolga Dincer <tolgadincer@gmail.com>
Date: Wed, 14 Dec 2022 15:09:48 -0600
Subject: [PATCH 24/24] final touches

---
 CHANGELOG.md                         | 4 ++--
 element_interface/extract_trigger.py | 2 +-
 element_interface/version.py         | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 83f13a3..48b9186 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,7 +2,7 @@
 
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
-## [0.3.1] - Unreleased
+## [0.4.0] - 2022-12-14
 
 + Add - mkdocs documentation
 + Add - improved docstrings for mkdocs
@@ -37,7 +37,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 
 + Add - Readers for: `ScanImage`, `Suite2p`, `CaImAn`.
 
-[0.3.1]: https://github.com/datajoint/element-interface/releases/tag/0.3.1
+[0.4.0]: https://github.com/datajoint/element-interface/releases/tag/0.4.0
 [0.3.0]: https://github.com/datajoint/element-interface/releases/tag/0.3.0
 [0.2.1]: https://github.com/datajoint/element-interface/releases/tag/0.2.1
 [0.2.0]: https://github.com/datajoint/element-interface/releases/tag/0.2.0
diff --git a/element_interface/extract_trigger.py b/element_interface/extract_trigger.py
index 94db2e8..7541204 100644
--- a/element_interface/extract_trigger.py
+++ b/element_interface/extract_trigger.py
@@ -62,7 +62,7 @@ def write_matlab_run_script(self):
                         for k, v in self.parameters.items()
                     ]
                 ),
-                scanfile=self.scanfile,
+                scanfile=self.scanfile.as_posix(),
                 output_fullpath=self.output_fullpath.as_posix(),
             )
         ).lstrip()
diff --git a/element_interface/version.py b/element_interface/version.py
index 5c90a7e..eb3c802 100644
--- a/element_interface/version.py
+++ b/element_interface/version.py
@@ -1,3 +1,3 @@
 """Package metadata"""
 
-__version__ = "0.3.1"
+__version__ = "0.4.0"