From cd0161b9f115109c78be89fe60e0b8005d57ef94 Mon Sep 17 00:00:00 2001
From: Aleksandra Nenadic <a.nenadic@manchester.ac.uk>
Date: Wed, 10 Apr 2024 10:37:54 +0100
Subject: [PATCH 01/12] Added full analysis code

---
 inflammation-analysis.py     | 11 ++++++++++-
 inflammation/compute_data.py | 31 +++++++++++++++++++++++++++++++
 2 files changed, 41 insertions(+), 1 deletion(-)
 create mode 100644 inflammation/compute_data.py

diff --git a/inflammation-analysis.py b/inflammation-analysis.py
index 1ca0132f7..b619ec7f6 100644
--- a/inflammation-analysis.py
+++ b/inflammation-analysis.py
@@ -2,8 +2,10 @@
 """Software for managing and analysing patients' inflammation data in our imaginary hospital."""
 
 import argparse
+import os
 
 from inflammation import models, views
+from inflammation.compute_data import analyse_data
 
 
 def main(args):
@@ -17,8 +19,13 @@ def main(args):
     if not isinstance(InFiles, list):
         InFiles = [args.infiles]
 
+    print("infiles: " + str(InFiles))
 
-    for filename in InFiles:
+    if args.full_data_analysis:
+        analyse_data(os.path.dirname(InFiles[1]))
+        return
+
+    for filename in InFiles[1:]:
         inflammation_data = models.load_csv(filename)
 
         view_data = {'average': models.daily_mean(inflammation_data), 'max': models.daily_max(inflammation_data), 'min': models.daily_min(inflammation_data)}
@@ -34,6 +41,8 @@ def main(args):
         nargs='+',
         help='Input CSV(s) containing inflammation series for each patient')
 
+    parser.add_argument('--full-data-analysis', action='store_true', dest='full_data_analysis')
+
     args = parser.parse_args()
 
     main(args)
diff --git a/inflammation/compute_data.py b/inflammation/compute_data.py
new file mode 100644
index 000000000..47730326f
--- /dev/null
+++ b/inflammation/compute_data.py
@@ -0,0 +1,31 @@
+"""Module containing mechanism for calculating standard deviation between datasets.
+"""
+
+import glob
+import os
+import numpy as np
+
+from inflammation import models, views
+
+
+def analyse_data(data_dir):
+    """Calculate the standard deviation by day between datasets
+
+    Gets all the inflammation csvs within a directory, works out the mean
+    inflammation value for each day across all datasets, then graphs the
+    standard deviation of these means."""
+    data_file_paths = glob.glob(os.path.join(data_dir, 'inflammation*.csv'))
+    if len(data_file_paths) == 0:
+        raise ValueError(f"No inflammation csv's found in path {data_dir}")
+    data = map(models.load_csv, data_file_paths)
+
+
+    means_by_day = map(models.daily_mean, data)
+    means_by_day_matrix = np.stack(list(means_by_day))
+
+    daily_standard_deviation = np.std(means_by_day_matrix, axis=0)
+
+    graph_data = {
+        'standard deviation by day': daily_standard_deviation,
+    }
+    views.visualize(graph_data)
\ No newline at end of file

From 407e1bb15a0024a80dd7cff0d3eae312e38938ef Mon Sep 17 00:00:00 2001
From: Aleksandra Nenadic <a.nenadic@manchester.ac.uk>
Date: Fri, 12 Apr 2024 11:37:46 +0100
Subject: [PATCH 02/12] Improved formatting and documentation

---
 inflammation-analysis.py     | 12 +++++-------
 inflammation/compute_data.py | 10 +++++-----
 2 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/inflammation-analysis.py b/inflammation-analysis.py
index b619ec7f6..2a62ba60a 100644
--- a/inflammation-analysis.py
+++ b/inflammation-analysis.py
@@ -19,13 +19,8 @@ def main(args):
     if not isinstance(InFiles, list):
         InFiles = [args.infiles]
 
-    print("infiles: " + str(InFiles))
 
-    if args.full_data_analysis:
-        analyse_data(os.path.dirname(InFiles[1]))
-        return
-
-    for filename in InFiles[1:]:
+    for filename in InFiles:
         inflammation_data = models.load_csv(filename)
 
         view_data = {'average': models.daily_mean(inflammation_data), 'max': models.daily_max(inflammation_data), 'min': models.daily_min(inflammation_data)}
@@ -41,7 +36,10 @@ def main(args):
         nargs='+',
         help='Input CSV(s) containing inflammation series for each patient')
 
-    parser.add_argument('--full-data-analysis', action='store_true', dest='full_data_analysis')
+    parser.add_argument(
+        '--full-data-analysis',
+        action='store_true',
+        dest='full_data_analysis')
 
     args = parser.parse_args()
 
diff --git a/inflammation/compute_data.py b/inflammation/compute_data.py
index 47730326f..db3840d14 100644
--- a/inflammation/compute_data.py
+++ b/inflammation/compute_data.py
@@ -9,14 +9,14 @@
 
 
 def analyse_data(data_dir):
-    """Calculate the standard deviation by day between datasets
+    """Calculates the standard deviation by day between datasets.
 
-    Gets all the inflammation csvs within a directory, works out the mean
-    inflammation value for each day across all datasets, then graphs the
-    standard deviation of these means."""
+    Gets all the inflammation data from CSV files within a directory,
+    works out the mean inflammation value for each day across all datasets,
+    then plots the graphs of standard deviation of these means."""
     data_file_paths = glob.glob(os.path.join(data_dir, 'inflammation*.csv'))
     if len(data_file_paths) == 0:
-        raise ValueError(f"No inflammation csv's found in path {data_dir}")
+        raise ValueError(f"No inflammation data CSV files found in path {data_dir}")
     data = map(models.load_csv, data_file_paths)
 
 

From 8a281d8fe1897105e903ed22632964add555f925 Mon Sep 17 00:00:00 2001
From: Steve Crouch <s.crouch@software.ac.uk>
Date: Thu, 25 Apr 2024 13:32:17 +0100
Subject: [PATCH 03/12] Update with revised version from thomaskileyukaea

---
 inflammation-analysis.py | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/inflammation-analysis.py b/inflammation-analysis.py
index 2a62ba60a..df03d4cd5 100644
--- a/inflammation-analysis.py
+++ b/inflammation-analysis.py
@@ -15,18 +15,27 @@ def main(args):
     - selecting the necessary models and views for the current task
     - passing data between models and views
     """
-    InFiles = args.infiles
-    if not isinstance(InFiles, list):
-        InFiles = [args.infiles]
+    infiles = args.infiles
+    if not isinstance(infiles, list):
+        infiles = [args.infiles]
 
 
-    for filename in InFiles:
+    if args.full_data_analysis:
+        analyse_data(os.path.dirname(infiles[0]))
+        return
+
+    for filename in infiles:
         inflammation_data = models.load_csv(filename)
 
-        view_data = {'average': models.daily_mean(inflammation_data), 'max': models.daily_max(inflammation_data), 'min': models.daily_min(inflammation_data)}
+        view_data = {
+            'average': models.daily_mean(inflammation_data),
+            'max': models.daily_max(inflammation_data),
+            'min': models.daily_min(inflammation_data)
+        }
 
         views.visualize(view_data)
 
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         description='A basic patient inflammation data management system')

From 3030e15cee4141922f49eef6bf9e4d1f490bc4c7 Mon Sep 17 00:00:00 2001
From: Steven C Chan <80276802+SCChan21@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:23:09 +0000
Subject: [PATCH 04/12] Breaking analyse_data up

---
 inflammation/compute_data.py | 30 ++++++++++++++++++++++++------
 1 file changed, 24 insertions(+), 6 deletions(-)

diff --git a/inflammation/compute_data.py b/inflammation/compute_data.py
index db3840d14..f1615dcba 100644
--- a/inflammation/compute_data.py
+++ b/inflammation/compute_data.py
@@ -8,24 +8,42 @@
 from inflammation import models, views
 
 
+def compute_sdev(data, axis=0):
+    """
+    Compute standard deviation
+    """
+    return np.std(data, axis=axis)
+
+
+def compute_stacked_means_by_day(data):
+    """
+    Apply models.daily_mean to data and np.stack them.
+    """
+    means_by_day = map(models.daily_mean, data)
+    return np.stack(list(means_by_day))
+
+
+def compute_daily_sdev(data):
+    means_by_day_matrix = compute_stacked_means_by_day(data)
+    return compute_sdev(compute_daily_sdev)
+
+
 def analyse_data(data_dir):
     """Calculates the standard deviation by day between datasets.
 
     Gets all the inflammation data from CSV files within a directory,
     works out the mean inflammation value for each day across all datasets,
     then plots the graphs of standard deviation of these means."""
+
     data_file_paths = glob.glob(os.path.join(data_dir, 'inflammation*.csv'))
     if len(data_file_paths) == 0:
         raise ValueError(f"No inflammation data CSV files found in path {data_dir}")
-    data = map(models.load_csv, data_file_paths)
 
-
-    means_by_day = map(models.daily_mean, data)
-    means_by_day_matrix = np.stack(list(means_by_day))
-
-    daily_standard_deviation = np.std(means_by_day_matrix, axis=0)
+    data = map(models.load_csv, data_file_paths)
+    daily_standard_deviation = compute_daily_sdev(data)
 
     graph_data = {
         'standard deviation by day': daily_standard_deviation,
     }
+
     views.visualize(graph_data)
\ No newline at end of file

From 687fb103440c82f182ff8236748ad202a2ca0db3 Mon Sep 17 00:00:00 2001
From: Steven C Chan <80276802+SCChan21@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:23:43 +0000
Subject: [PATCH 05/12] Breaking analyse_data up

---
 inflammation/compute_data.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inflammation/compute_data.py b/inflammation/compute_data.py
index f1615dcba..4948f9e3e 100644
--- a/inflammation/compute_data.py
+++ b/inflammation/compute_data.py
@@ -25,7 +25,7 @@ def compute_stacked_means_by_day(data):
 
 def compute_daily_sdev(data):
     means_by_day_matrix = compute_stacked_means_by_day(data)
-    return compute_sdev(compute_daily_sdev)
+    return compute_sdev(means_by_day_matrix)
 
 
 def analyse_data(data_dir):

From 75d85f2de2d39063f35ebc1b84c78293543ddb6e Mon Sep 17 00:00:00 2001
From: Steven C Chan <80276802+SCChan21@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:48:25 +0000
Subject: [PATCH 06/12] Abstracted compute_data csv loading

---
 inflammation/compute_data.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/inflammation/compute_data.py b/inflammation/compute_data.py
index 4948f9e3e..d9e52692d 100644
--- a/inflammation/compute_data.py
+++ b/inflammation/compute_data.py
@@ -28,6 +28,14 @@ def compute_daily_sdev(data):
     return compute_sdev(means_by_day_matrix)
 
 
+class CSVStuff:
+    def __init__(self, csv_file_list):
+        self.csv_filenames = csv_file_list
+
+    def load_data(self):
+        return map(models.load_csv, self.csv_filenames)
+
+
 def analyse_data(data_dir):
     """Calculates the standard deviation by day between datasets.
 
@@ -39,7 +47,7 @@ def analyse_data(data_dir):
     if len(data_file_paths) == 0:
         raise ValueError(f"No inflammation data CSV files found in path {data_dir}")
 
-    data = map(models.load_csv, data_file_paths)
+    data = CSVStuff(data_file_paths).load_data()
     daily_standard_deviation = compute_daily_sdev(data)
 
     graph_data = {

From 43be41941f23d72b6a018b78cd5ed55c6d4ce13c Mon Sep 17 00:00:00 2001
From: Steven C Chan <80276802+SCChan21@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:58:29 +0000
Subject: [PATCH 07/12] Abstracted compute_data csv loading

---
 inflammation/compute_data.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/inflammation/compute_data.py b/inflammation/compute_data.py
index d9e52692d..81658fd60 100644
--- a/inflammation/compute_data.py
+++ b/inflammation/compute_data.py
@@ -28,9 +28,15 @@ def compute_daily_sdev(data):
     return compute_sdev(means_by_day_matrix)
 
 
-class CSVStuff:
-    def __init__(self, csv_file_list):
+class CSVDataSrc:
+    def __init__(self, data_dir):
+        csv_file_list = glob.glob(os.path.join(data_dir, 'inflammation*.csv'))
+        csv_file_list.sort()
+        self.data_dir = data_dir
+        if len(csv_file_list) == 0:
+            raise ValueError(f"No inflammation data CSV files found in path {data_dir}")
         self.csv_filenames = csv_file_list
+        print(self.csv_filenames[0], self.csv_filenames[-1])
 
     def load_data(self):
         return map(models.load_csv, self.csv_filenames)
@@ -43,11 +49,7 @@ def analyse_data(data_dir):
     works out the mean inflammation value for each day across all datasets,
     then plots the graphs of standard deviation of these means."""
 
-    data_file_paths = glob.glob(os.path.join(data_dir, 'inflammation*.csv'))
-    if len(data_file_paths) == 0:
-        raise ValueError(f"No inflammation data CSV files found in path {data_dir}")
-
-    data = CSVStuff(data_file_paths).load_data()
+    data = CSVDataSrc(data_dir).load_data()
     daily_standard_deviation = compute_daily_sdev(data)
 
     graph_data = {

From cdc05bd6689c74fc95be264be1f000b8292f767d Mon Sep 17 00:00:00 2001
From: Steven C Chan <80276802+SCChan21@users.noreply.github.com>
Date: Fri, 17 Jan 2025 12:25:33 +0000
Subject: [PATCH 08/12] Not-really-json file tests

---
 data/inflammation-01.json    | 60 ++++++++++++++++++++++++++++++++++++
 data/inflammation-02.json    | 60 ++++++++++++++++++++++++++++++++++++
 data/inflammation-03.json    | 60 ++++++++++++++++++++++++++++++++++++
 data/inflammation-04.json    | 60 ++++++++++++++++++++++++++++++++++++
 data/inflammation-05.json    | 60 ++++++++++++++++++++++++++++++++++++
 inflammation-analysis.py     | 12 ++++++--
 inflammation/compute_data.py | 28 ++++++++++++-----
 inflammation/models.py       | 12 +++++++-
 8 files changed, 341 insertions(+), 11 deletions(-)
 create mode 100644 data/inflammation-01.json
 create mode 100644 data/inflammation-02.json
 create mode 100644 data/inflammation-03.json
 create mode 100644 data/inflammation-04.json
 create mode 100644 data/inflammation-05.json

diff --git a/data/inflammation-01.json b/data/inflammation-01.json
new file mode 100644
index 000000000..07a2e6040
--- /dev/null
+++ b/data/inflammation-01.json
@@ -0,0 +1,60 @@
+0,0,1,3,1,2,4,7,8,3,3,3,10,5,7,4,7,7,12,18,6,13,11,11,7,7,4,6,8,8,4,4,5,7,3,4,2,3,0,0
+0,1,2,1,2,1,3,2,2,6,10,11,5,9,4,4,7,16,8,6,18,4,12,5,12,7,11,5,11,3,3,5,4,4,5,5,1,1,0,1
+0,1,1,3,3,2,6,2,5,9,5,7,4,5,4,15,5,11,9,10,19,14,12,17,7,12,11,7,4,2,10,5,4,2,2,3,2,2,1,1
+0,0,2,0,4,2,2,1,6,7,10,7,9,13,8,8,15,10,10,7,17,4,4,7,6,15,6,4,9,11,3,5,6,3,3,4,2,3,2,1
+0,1,1,3,3,1,3,5,2,4,4,7,6,5,3,10,8,10,6,17,9,14,9,7,13,9,12,6,7,7,9,6,3,2,2,4,2,0,1,1
+0,0,1,2,2,4,2,1,6,4,7,6,6,9,9,15,4,16,18,12,12,5,18,9,5,3,10,3,12,7,8,4,7,3,5,4,4,3,2,1
+0,0,2,2,4,2,2,5,5,8,6,5,11,9,4,13,5,12,10,6,9,17,15,8,9,3,13,7,8,2,8,8,4,2,3,5,4,1,1,1
+0,0,1,2,3,1,2,3,5,3,7,8,8,5,10,9,15,11,18,19,20,8,5,13,15,10,6,10,6,7,4,9,3,5,2,5,3,2,2,1
+0,0,0,3,1,5,6,5,5,8,2,4,11,12,10,11,9,10,17,11,6,16,12,6,8,14,6,13,10,11,4,6,4,7,6,3,2,1,0,0
+0,1,1,2,1,3,5,3,5,8,6,8,12,5,13,6,13,8,16,8,18,15,16,14,12,7,3,8,9,11,2,5,4,5,1,4,1,2,0,0
+0,1,0,0,4,3,3,5,5,4,5,8,7,10,13,3,7,13,15,18,8,15,15,16,11,14,12,4,10,10,4,3,4,5,5,3,3,2,2,1
+0,1,0,0,3,4,2,7,8,5,2,8,11,5,5,8,14,11,6,11,9,16,18,6,12,5,4,3,5,7,8,3,5,4,5,5,4,0,1,1
+0,0,2,1,4,3,6,4,6,7,9,9,3,11,6,12,4,17,13,15,13,12,8,7,4,7,12,9,5,6,5,4,7,3,5,4,2,3,0,1
+0,0,0,0,1,3,1,6,6,5,5,6,3,6,13,3,10,13,9,16,15,9,11,4,6,4,11,11,12,3,5,8,7,4,6,4,1,3,0,0
+0,1,2,1,1,1,4,1,5,2,3,3,10,7,13,5,7,17,6,9,12,13,10,4,12,4,6,7,6,10,8,2,5,1,3,4,2,0,2,0
+0,1,1,0,1,2,4,3,6,4,7,5,5,7,5,10,7,8,18,17,9,8,12,11,11,11,14,6,11,2,10,9,5,6,5,3,4,2,2,0
+0,0,0,0,2,3,6,5,7,4,3,2,10,7,9,11,12,5,12,9,13,19,14,17,5,13,8,11,5,10,9,8,7,5,3,1,4,0,2,1
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diff --git a/data/inflammation-02.json b/data/inflammation-02.json
new file mode 100644
index 000000000..e30a9b275
--- /dev/null
+++ b/data/inflammation-02.json
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diff --git a/data/inflammation-03.json b/data/inflammation-03.json
new file mode 100644
index 000000000..c301c9b66
--- /dev/null
+++ b/data/inflammation-03.json
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diff --git a/data/inflammation-04.json b/data/inflammation-04.json
new file mode 100644
index 000000000..219ae8149
--- /dev/null
+++ b/data/inflammation-04.json
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diff --git a/data/inflammation-05.json b/data/inflammation-05.json
new file mode 100644
index 000000000..25ef868c6
--- /dev/null
+++ b/data/inflammation-05.json
@@ -0,0 +1,60 @@
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+0,0,0,2,1,4,2,1,7,5,9,8,8,6,9,3,11,9,17,6,10,11,17,16,16,10,13,13,6,10,6,9,2,2,2,1,2,0,0,0
+0,0,1,2,4,4,3,5,3,3,2,6,9,13,6,13,6,4,15,6,15,11,6,14,6,7,13,4,3,11,4,4,8,4,1,3,2,1,0,0
+0,0,2,2,4,5,5,1,5,2,9,6,6,7,14,15,11,17,13,19,18,18,16,4,7,15,6,5,6,8,2,4,6,7,5,5,2,2,2,0
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+0,0,0,2,1,5,4,2,5,6,7,6,6,9,3,15,9,11,14,14,14,10,5,10,11,11,12,10,6,4,8,7,4,5,2,2,3,3,1,1
+0,0,0,1,1,1,6,3,3,4,7,7,9,7,14,3,7,8,12,7,6,7,7,6,8,14,4,6,8,10,4,3,3,5,6,5,2,3,1,0
+0,0,2,2,4,3,4,2,8,6,2,8,12,9,5,10,11,16,16,14,9,15,7,17,13,11,10,10,3,4,3,6,5,7,3,3,2,2,0,0
+0,0,2,0,3,1,4,4,4,4,9,11,4,9,12,15,4,13,9,13,11,17,5,15,8,6,8,3,12,8,7,3,2,7,3,3,4,0,0,1
+0,0,0,1,1,3,1,5,4,8,8,5,9,3,14,15,7,11,10,17,20,8,13,10,9,7,6,8,3,2,4,4,3,3,1,1,4,0,0,1
+0,1,0,1,4,5,3,7,2,3,9,7,3,11,3,12,6,16,16,13,12,8,14,17,9,13,8,8,9,4,2,8,5,6,1,5,3,2,0,1
+0,0,0,1,4,1,5,6,4,9,3,5,7,9,11,15,10,9,8,18,18,19,12,4,6,4,11,11,5,11,10,3,8,5,4,1,4,2,0,1
+0,1,1,0,3,4,1,7,7,4,2,8,7,12,14,8,6,8,12,15,18,8,12,17,14,4,12,7,10,8,5,2,8,4,2,4,2,0,1,0
+0,1,1,2,2,4,5,2,7,9,7,6,10,9,9,4,16,4,11,12,6,10,16,12,7,11,14,8,12,7,6,7,8,1,4,4,1,0,2,0
+0,0,1,3,3,1,3,3,3,2,6,9,6,3,13,15,7,16,17,15,10,16,4,17,8,13,4,10,12,3,5,7,6,6,4,3,4,0,1,0
+0,0,0,3,2,3,2,5,8,8,7,4,8,6,8,4,8,4,4,4,9,19,8,9,7,8,10,12,4,11,8,9,6,6,6,3,3,1,1,0
+0,0,1,2,3,5,6,4,8,4,10,7,3,6,12,6,6,15,9,19,7,15,16,11,9,9,9,6,8,2,7,7,4,5,6,4,4,0,1,1
+0,0,1,0,1,3,5,5,5,3,4,9,10,5,6,5,13,9,4,6,5,16,5,11,5,12,10,5,7,10,6,9,6,3,4,5,3,2,0,0
+0,1,1,1,2,2,4,1,2,8,9,8,5,11,3,12,4,7,6,7,5,5,11,12,7,12,5,8,6,10,6,7,4,2,1,4,2,1,0,1
+0,0,2,1,3,5,6,2,3,8,6,6,3,3,11,5,4,14,10,11,5,15,10,15,13,12,13,10,3,2,2,5,7,6,1,5,4,0,1,1
+0,1,2,3,4,5,1,2,2,6,7,2,4,8,8,14,14,9,13,13,9,8,10,17,14,15,13,13,9,4,2,6,6,3,2,5,4,1,2,1
+0,0,1,0,3,4,4,3,3,9,3,2,8,11,8,7,9,15,7,19,16,15,6,16,5,13,9,11,5,3,6,9,5,3,3,2,4,1,0,1
diff --git a/inflammation-analysis.py b/inflammation-analysis.py
index df03d4cd5..7a51089b1 100644
--- a/inflammation-analysis.py
+++ b/inflammation-analysis.py
@@ -6,7 +6,7 @@
 
 from inflammation import models, views
 from inflammation.compute_data import analyse_data
-
+from inflammation.compute_data import CSVDataSrc, JSONDataSrc
 
 def main(args):
     """The MVC Controller of the patient inflammation data system.
@@ -21,7 +21,15 @@ def main(args):
 
 
     if args.full_data_analysis:
-        analyse_data(os.path.dirname(infiles[0]))
+        data_src = os.path.dirname(infiles[0])
+        _, data_ext = os.path.splitext(infiles[0])
+        if data_ext == ".csv":
+            src_type = CSVDataSrc
+        elif data_ext == ".json":
+            src_type = JSONDataSrc
+        else:
+            raise ValueError('Unknown extension: {data_ext}')
+        analyse_data(data_src, src_type=src_type)
         return
 
     for filename in infiles:
diff --git a/inflammation/compute_data.py b/inflammation/compute_data.py
index 81658fd60..d980e6fa8 100644
--- a/inflammation/compute_data.py
+++ b/inflammation/compute_data.py
@@ -30,26 +30,38 @@ def compute_daily_sdev(data):
 
 class CSVDataSrc:
     def __init__(self, data_dir):
-        csv_file_list = glob.glob(os.path.join(data_dir, 'inflammation*.csv'))
-        csv_file_list.sort()
         self.data_dir = data_dir
+
+    def load_data(self):
+        csv_file_list = glob.glob(os.path.join(self.data_dir, 'inflammation*.csv'))
+        csv_file_list.sort()
         if len(csv_file_list) == 0:
-            raise ValueError(f"No inflammation data CSV files found in path {data_dir}")
-        self.csv_filenames = csv_file_list
-        print(self.csv_filenames[0], self.csv_filenames[-1])
+            raise ValueError(f"No inflammation data CSV files found in path {self.data_dir}")
+        print('Loading : ', csv_file_list[0], csv_file_list[-1])
+        return map(models.load_csv, csv_file_list)
+
+
+class JSONDataSrc:
+    def __init__(self, data_dir):
+        self.data_dir = data_dir
 
     def load_data(self):
-        return map(models.load_csv, self.csv_filenames)
+        json_file_list = glob.glob(os.path.join(self.data_dir, 'inflammation*.json'))
+        json_file_list.sort()
+        if len(json_file_list) == 0:
+            raise ValueError(f"No inflammation data CSV files found in path {self.data_dir}")
+        print('Loading : ', json_file_list[0], json_file_list[-1])
+        return map(models.load_csv, json_file_list)
 
 
-def analyse_data(data_dir):
+def analyse_data(data_dir, src_type=CSVDataSrc):
     """Calculates the standard deviation by day between datasets.
 
     Gets all the inflammation data from CSV files within a directory,
     works out the mean inflammation value for each day across all datasets,
     then plots the graphs of standard deviation of these means."""
 
-    data = CSVDataSrc(data_dir).load_data()
+    data = src_type(data_dir).load_data()
     daily_standard_deviation = compute_daily_sdev(data)
 
     graph_data = {
diff --git a/inflammation/models.py b/inflammation/models.py
index 5169ac42d..717116cfb 100644
--- a/inflammation/models.py
+++ b/inflammation/models.py
@@ -8,7 +8,7 @@
 """
 
 import numpy as np
-
+import json
 
 def load_csv(filename):  
     """Load a Numpy array from a CSV
@@ -18,6 +18,16 @@ def load_csv(filename):
     return np.loadtxt(fname=filename, delimiter=',')
 
 
+def load_json(filename,
+              json_key="observations"):
+    """Load a Numpy array from a JSON
+
+    :param filename: Filename of JSON to load
+    """
+    json_dict = json.loads(filename)
+    return [np.array(dats) for dats in json_dict[json_key]]
+
+
 def daily_mean(data):
     """Calculate the daily mean of a 2d inflammation data array."""
     return np.mean(data, axis=0)

From f6a64a5bb2fbdefef0ec7ddfda10d85f118ebc6f Mon Sep 17 00:00:00 2001
From: Steven C Chan <80276802+SCChan21@users.noreply.github.com>
Date: Fri, 17 Jan 2025 15:00:00 +0000
Subject: [PATCH 09/12] Resolve conflicts?

---
 inflammation-analysis.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/inflammation-analysis.py b/inflammation-analysis.py
index 7a51089b1..41c7e8457 100644
--- a/inflammation-analysis.py
+++ b/inflammation-analysis.py
@@ -15,14 +15,14 @@ def main(args):
     - selecting the necessary models and views for the current task
     - passing data between models and views
     """
-    infiles = args.infiles
-    if not isinstance(infiles, list):
-        infiles = [args.infiles]
+    in_files = args.infiles
+    if not isinstance(in_files, list):
+        in_files = [args.infiles]
 
 
     if args.full_data_analysis:
-        data_src = os.path.dirname(infiles[0])
-        _, data_ext = os.path.splitext(infiles[0])
+        data_src = os.path.dirname(in_files[0])
+        _, data_ext = os.path.splitext(in_files[0])
         if data_ext == ".csv":
             src_type = CSVDataSrc
         elif data_ext == ".json":

From c6ac18ca0c416360e80ac1617143bb1da14889de Mon Sep 17 00:00:00 2001
From: Steven C Chan <80276802+SCChan21@users.noreply.github.com>
Date: Fri, 17 Jan 2025 15:01:35 +0000
Subject: [PATCH 10/12] Resolve conflicts?

---
 inflammation-analysis.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inflammation-analysis.py b/inflammation-analysis.py
index 41c7e8457..b9062fc7f 100644
--- a/inflammation-analysis.py
+++ b/inflammation-analysis.py
@@ -32,7 +32,7 @@ def main(args):
         analyse_data(data_src, src_type=src_type)
         return
 
-    for filename in infiles:
+    for filename in in_files:
         inflammation_data = models.load_csv(filename)
 
         view_data = {

From 34819549eb56f397d466f42563486750397f263b Mon Sep 17 00:00:00 2001
From: Steven C Chan <80276802+SCChan21@users.noreply.github.com>
Date: Fri, 17 Jan 2025 15:06:14 +0000
Subject: [PATCH 11/12] Resolve conflicts?

---
 inflammation-analysis.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inflammation-analysis.py b/inflammation-analysis.py
index b9062fc7f..de59d3778 100644
--- a/inflammation-analysis.py
+++ b/inflammation-analysis.py
@@ -38,7 +38,7 @@ def main(args):
         view_data = {
             'average': models.daily_mean(inflammation_data),
             'max': models.daily_max(inflammation_data),
-            'min': models.daily_min(inflammation_data)
+            'min': models.daily_min(inflammation_data),
         }
 
         views.visualize(view_data)

From 8548894b6784ea901c4f1d673be3f5755c12ff31 Mon Sep 17 00:00:00 2001
From: Steven C Chan <80276802+SCChan21@users.noreply.github.com>
Date: Fri, 17 Jan 2025 15:09:12 +0000
Subject: [PATCH 12/12] Resolve conflicts?

---
 inflammation-analysis.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/inflammation-analysis.py b/inflammation-analysis.py
index de59d3778..9ceb4b409 100644
--- a/inflammation-analysis.py
+++ b/inflammation-analysis.py
@@ -36,9 +36,9 @@ def main(args):
         inflammation_data = models.load_csv(filename)
 
         view_data = {
-            'average': models.daily_mean(inflammation_data),
-            'max': models.daily_max(inflammation_data),
-            'min': models.daily_min(inflammation_data),
+            "average": models.daily_mean(inflammation_data),
+            "max": models.daily_max(inflammation_data),
+            "min": models.daily_min(inflammation_data),
         }
 
         views.visualize(view_data)