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167 changes: 150 additions & 17 deletions 02_activities/assignments/assignment_2.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -72,13 +72,81 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 44,
"metadata": {
"id": "n0m48JsS-nMC"
},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
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]
}
],
"source": [
"all_paths = [\n",
"\"\"\"\n",
"# all_paths = [\n",
" \"python/05_src/data/assignment_2_data/inflammation_01.csv\",\n",
" \"python/05_src/data/assignment_2_data/inflammation_02.csv\",\n",
" \"python/05_src/data/assignment_2_data/inflammation_03.csv\",\n",
Expand All @@ -91,12 +159,34 @@
" \"python/05_src/data/assignment_2_data/inflammation_10.csv\",\n",
" \"python/05_src/data/assignment_2_data/inflammation_11.csv\",\n",
" \"python/05_src/data/assignment_2_data/inflammation_12.csv\"\n",
"#]\n",
"\"\"\"\n",
"# # Absolute path to the inflammation data file \n",
"#r means raw string i.e Treat this string exactly as it's written, don't interpret any escape characters.\n",
"all_paths = [ \n",
" r\"C:\\Users\\mrfst\\DSI7-Task\\python\\python\\05_src\\data\\assignment_2_data\\inflammation_01.csv\",\n",
" r\"C:\\Users\\mrfst\\DSI7-Task\\python\\python\\05_src\\data\\assignment_2_data\\inflammation_02.csv\",\n",
" r\"C:\\Users\\mrfst\\DSI7-Task\\python\\python\\05_src\\data\\assignment_2_data\\inflammation_03.csv\",\n",
" r\"C:\\Users\\mrfst\\DSI7-Task\\python\\python\\05_src\\data\\assignment_2_data\\inflammation_04.csv\",\n",
" r\"C:\\Users\\mrfst\\DSI7-Task\\python\\python\\05_src\\data\\assignment_2_data\\inflammation_05.csv\",\n",
" r\"C:\\Users\\mrfst\\DSI7-Task\\python\\python\\05_src\\data\\assignment_2_data\\inflammation_06.csv\",\n",
" r\"C:\\Users\\mrfst\\DSI7-Task\\python\\python\\05_src\\data\\assignment_2_data\\inflammation_07.csv\",\n",
" r\"C:\\Users\\mrfst\\DSI7-Task\\python\\python\\05_src\\data\\assignment_2_data\\inflammation_08.csv\",\n",
" r\"C:\\Users\\mrfst\\DSI7-Task\\python\\python\\05_src\\data\\assignment_2_data\\inflammation_09.csv\",\n",
" r\"C:\\Users\\mrfst\\DSI7-Task\\python\\python\\05_src\\data\\assignment_2_data\\inflammation_10.csv\",\n",
" r\"C:\\Users\\mrfst\\DSI7-Task\\python\\python\\05_src\\data\\assignment_2_data\\inflammation_11.csv\",\n",
" r\"C:\\Users\\mrfst\\DSI7-Task\\python\\python\\05_src\\data\\assignment_2_data\\inflammation_12.csv\"\n",
"]\n",
"\n",
"with open(all_paths[0], 'r') as f:\n",
" # YOUR CODE HERE: Use the readline() or readlines() method to read the .csv file into a variable\n",
" \n",
" # YOUR CODE HERE: Iterate through the variable using a for loop and print each row for inspection"
" # Read all lines from the file\n",
" lines = f.readlines()\n",
" # YOUR CODE HERE: Iterate through the variable using a for loop and print each row for inspection\n",
" # Iterate through each line and print it\n",
" for row in lines:\n",
" #print(row)\n",
" print(row.strip()) # strip() removes any extra whitespace or newline characters\n",
" "
]
},
{
Expand Down Expand Up @@ -145,12 +235,18 @@
" # Implement the specific operation based on the 'operation' argument\n",
" if operation == 'mean':\n",
" # YOUR CODE HERE: Calculate the mean (average) number of flare-ups for each patient\n",
" # Calculate the mean (average) number of flare-ups for each patient\n",
" summary_values = np.mean(data, axis=1) # axis=1 means calculate along rows (patients)\n",
"\n",
" elif operation == 'max':\n",
" # YOUR CODE HERE: Calculate the maximum number of flare-ups experienced by each patient\n",
" # Calculate the maximum number of flare-ups experienced by each patient\n",
" summary_values = np.max(data, axis=1)\n",
"\n",
" elif operation == 'min':\n",
" # YOUR CODE HERE: Calculate the minimum number of flare-ups experienced by each patient\n",
" # Calculate the minimum number of flare-ups experienced by each patient\n",
" summary_values = np.min(data, axis=1)\n",
"\n",
" else:\n",
" # If the operation is not one of the expected values, raise an error\n",
Expand All @@ -165,14 +261,33 @@
"metadata": {
"id": "3TYo0-1SDLrd"
},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Length of data_min: 60\n",
"First few values: [0. 0. 0. 0. 0. 0.]\n"
]
}
],
"source": [
"#\n",
"# Test it out on the data file we read in and make sure the size is what we expect i.e., 60\n",
"# Your output for the first file should be 60\n",
"data_min = patient_summary(all_paths[0], 'min')\n",
"print(len(data_min))"
"#print(len(data_min))\n",
"print(f\"Length of data_min: {len(data_min)}\")\n",
"print(f\"First few values: {data_min[:6]}\") # show first few values to verify"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {
Expand Down Expand Up @@ -228,7 +343,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 47,
"metadata": {
"id": "_svDiRkdIwiT"
},
Expand All @@ -251,29 +366,46 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 48,
"metadata": {
"id": "LEYPM5v4JT0i"
},
"outputs": [],
"source": [
"# Define your function `detect_problems` here\n",
"#Detects if any patients have a mean inflammation score of 0\n",
"# Returns: bool: True if any patients have mean score of 0 (data issue), otherwise False\n",
"\n",
"def detect_problems(file_path):\n",
" #YOUR CODE HERE: Use patient_summary() to get the means and check_zeros() to check for zeros in the means\n",
"\n",
" return"
" # Use patient_summary() to get the means\n",
" mean_scores = patient_summary(file_path, 'mean')\n",
" # Use check_zeros() to check for zeros in the means\n",
" zeros_found = check_zeros(mean_scores) # \n",
" return zeros_found\n",
" "
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 49,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"False\n",
"False\n"
]
}
],
"source": [
"# Test out your code here\n",
"# Your output for the first file should be False\n",
"print(detect_problems(all_paths[0]))"
"#return bool: True if any patients have mean score of 0 (data issue), otherwise :false\n",
"print(detect_problems(all_paths[0]))\n",
"print(detect_problems(all_paths[1]))"
]
},
{
Expand Down Expand Up @@ -314,7 +446,8 @@
"provenance": []
},
"kernelspec": {
"display_name": "Python 3",
"display_name": "dsi_participant",
"language": "python",
"name": "python3"
},
"language_info": {
Expand All @@ -327,7 +460,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.8"
"version": "3.9.19"
}
},
"nbformat": 4,
Expand Down