def fit_reds(segments=[],
intensities=[],
mus=[],
sigmas=[],
N=25,
tolerance=1e-5):
alphas = [len(segments[k]) for k in range(3)]
alpha_norm = sum(alphas)
for k in range(3):
alphas[k] /= alpha_norm
likelihoods,alphas,mus,sigmas =\
gcps.maximize_likelihood(
intensities,
mus = mus,
sigmas = sigmas,
alphas = alphas,
N = args.N,
limit = args.tolerance,
K = 3)
barcode, levels = standards.lookup(plate, references)
_, _, r_value, _, _ = stats.linregress(levels, [math.exp(y) for y in mus])
return alphas, mus, sigmas, levels, r_value
def _gen_grades():
filedir = os.path.dirname(os.path.abspath(__file__))
if common.DEBUG: studentdir = './test/students'
else: studentdir = '../../../students'
studentdir = os.path.abspath(os.path.join(filedir, studentdir))
assignmentsfile = os.path.join(studentdir, 'assignments.gen.py')
scandir = os.path.join(studentdir, 'scans')
# .........................................................................
name2cwid = {
v['github'].lower(): k
for k, v in students.students.items() if 'github' in v
}
grades = {
cwid: OrderedDict([
('extra credit', 0),
('overall', None),
('predictions', OrderedDict()),
] + [((
g,
s,
), OrderedDict()) for g, ss in standards.groups.items() for s in ss])
for cwid in students.students
}
# .........................................................................
# from github
github = github3.GitHub()
try:
for r in sorted([r.name for r in github.iter_user_repos(common.org)]):
if r in ('course-materials', ): continue
assignment = 'a' + r[-2:]
for cwid in students.students:
grades[cwid][('assignment completion', '')][assignment] = None
for pr in github.iter_repo_issues(common.org, r, state='all'):
name = pr.user.login
if name not in name2cwid: continue
grades[name2cwid[name]] \
[('assignment completion', '')] \
[assignment] = True
with open(assignmentsfile, 'w') as f:
f.write(
repr({
cwid: grades[cwid][('assignment completion', '')]
for cwid in grades
}))
except (requests.exceptions.ConnectionError, github3.models.GitHubError):
assignments = eval(open(assignmentsfile).read())
none = OrderedDict([(a, None)
for a in assignments[list(assignments.keys())[0]]])
for cwid in grades:
if cwid in assignments:
grades[cwid][('assignment completion', '')] = assignments[cwid]
else:
grades[cwid][('assignment completion', '')] = none
# .........................................................................
# from scans
for d in sorted(os.listdir(scandir)):
if d.startswith('.'): continue
i = Namespace()
(i.date, i.assessment, i.standards) = d.split(',', maxsplit=2)
i.standards = [standards.lookup(s) for s in i.standards.split(',')]
for cwid in students.students:
for sta in i.standards:
grades[cwid][sta][i.assessment] = None
for f in os.listdir(os.path.join(scandir, d)):
if f.startswith('.'): continue
(i.name, i.scores) = \
f.split('.',maxsplit=1)[0].split(',', maxsplit=1)
i.scores = i.scores.split(',')
if '' in i.scores:
raise Error('WARNING: empty score in' + ' "' +
os.path.join(d, f) + '"')
if len(i.scores) != len(i.standards):
raise Error('WARNING: mismatch in number of scores for' +
' "' + os.path.join(d, f) + '"')
i.scores = [
None if s == 'x' else
3.5 if s == '5' else 3.75 if s == '7' else int(s)
for s in i.scores
]
for sta, sco in zip(i.standards, i.scores):
grades[students.lookup(i.name)][sta][i.assessment] = sco
# .........................................................................
# from file
private = common.importfile(os.path.join(studentdir, 'grades.py'))
for cwid in private.grades:
if cwid in grades: grades[cwid].update(private.grades[cwid])
else: grades[cwid] = private.grades[cwid]
# .........................................................................
for cwid in grades:
overall = 0
maximum = 0
for sta, assessments in grades[cwid].items():
if isinstance(sta, str): continue
scos = [sco for sco in assessments.values() if sco is not None]
if sta == ('assignment completion', ''):
sco = len(scos) / len(assessments) if len(
assessments) > 0 else 0
assessments['overall'] = sco
overall += sco * standards.multipliers[sta]
maximum += standards.multipliers[sta]
continue
if len(scos) == 0:
assessments['overall'] = None
else:
if len(scos) == 1 or scos[-1] >= scos[-2]:
sco = scos[-1]
else: # scos[-1] < scos[-2]
sco = [
sco for sco in [1, 2, 3, 3.5, 3.75, 4]
if (scos[-1] + scos[-2]) / 2 <= sco
][0]
assessments['overall'] = sco
if sco >= 3:
overall += sco / 4 * standards.multipliers[sta]
maximum += standards.multipliers[sta]
ec = grades[cwid]['extra credit'] * 0.002
if grades[cwid]['overall'] is None:
grades[cwid]['overall'] = overall + ec
grades[cwid]['predictions']['current grade'] = grades[cwid]['overall']
if maximum == 0:
grades[cwid]['predictions']['average'] = None
grades[cwid]['predictions']['maximum without reassessing'] = None
else:
grades[cwid]['predictions']['average'] = overall / maximum
grades[cwid]['predictions']['maximum without reassessing'] = \
1 - maximum + overall + ec
# .........................................................................
return grades
def _gen_grades():
org = '2016-spring-csuf-benblazak-cpsc-121'
filedir = os.path.dirname(os.path.abspath(__file__))
if common.DEBUG: studentdir = './test/students'
else: studentdir = '../../../students'
studentdir = os.path.abspath(os.path.join(filedir, studentdir))
assignmentsfile = os.path.join(studentdir, 'assignments.gen.py')
scandir = os.path.join(studentdir, 'scans')
# .........................................................................
name2cwid = {
v['github'].lower():k
for k,v in students.students.items()
if 'github' in v
}
grades = {
cwid: OrderedDict( [ ('extra credit', 0) ] + [
((g,s,),OrderedDict())
for g,ss in standards.groups.items()
for s in ss
])
for cwid in students.students
}
# .........................................................................
github = github3.GitHub()
try:
for r in sorted([ r.name for r in github.iter_user_repos(org) ]):
if r in ( 'course-materials', ): continue
assignment = 'a' + r[-2:]
for cwid in students.students:
grades[cwid][('assignment completion', '')][assignment] = None
for pr in github.iter_repo_issues(org, r, state='all'):
name = pr.user.login
if name not in name2cwid: continue
grades[name2cwid[name]] \
[('assignment completion', '')] \
[assignment] = 4
with open(assignmentsfile, 'w') as f:
f.write(repr({
cwid: grades[cwid][('assignment completion', '')]
for cwid in grades
}))
except (requests.exceptions.ConnectionError, github3.models.GitHubError):
assignments = eval(open(assignmentsfile).read())
none = OrderedDict([
(a, None) for a in assignments[list(assignments.keys())[0]]
])
for cwid in grades:
if cwid in assignments:
grades[cwid][('assignment completion', '')] = assignments[cwid]
else:
grades[cwid][('assignment completion', '')] = none
# .........................................................................
for d in sorted(os.listdir(scandir)):
if d.startswith('.'): continue
i = Namespace()
(i.date, i.assessment, i.standards) = d.split(',', maxsplit=2)
i.standards = [ standards.lookup(s) for s in i.standards.split(',') ]
for cwid in students.students:
for sta in i.standards:
grades[cwid][sta][i.assessment] = None
for f in os.listdir(os.path.join(scandir, d)):
if f.startswith('.'): continue
(i.name, i.scores) = \
f.split('.',maxsplit=1)[0].split(',', maxsplit=1)
i.scores = [
None if s == '' else
3.5 if s == '5' else
3.75 if s == '7' else
int(s)
for s in i.scores.split(',')
]
for sta,sco in zip(i.standards,i.scores):
grades[students.lookup(i.name)][sta][i.assessment] = sco
# .........................................................................
# TODO: calculate overall grades
# .........................................................................
# TODO: update grades from other file
# .........................................................................
return grades
alphas = [len(segments[k]) for k in range(K)]
alpha_norm = sum(alphas)
for k in range(K):
alphas[k] /= alpha_norm
likelihoods,alphas,mus,sigmas =\
maximize_likelihood(
intensities,
mus = mus,
sigmas = sigmas,
alphas = alphas,
N = args.N,
limit = args.tolerance,
K = K)
if K == 3:
barcode, levels = standards.lookup(plate, references)
_, _, r_value, _, _ = stats.linregress(
levels, [math.exp(y) for y in mus])
print(f'Using standard for {barcode}, r_value={r_value}')
ax3 = plt.subplot(2, 2, 3)
ax3.plot(range(len(likelihoods)), likelihoods)
ax3.set_xlabel('Iteration')
ax3.set_ylabel('Log Likelihood')
ax4 = plt.subplot(2, 2, 4)
n, bins, _ = ax4.hist(intensities,
facecolor='g',
bins=100,
def _gen_grades():
filedir = os.path.dirname(os.path.abspath(__file__))
if common.DEBUG: studentdir = './test/students'
else: studentdir = '../../../students'
studentdir = os.path.abspath(os.path.join(filedir, studentdir))
assignmentsfile = os.path.join(studentdir, 'assignments.gen.py')
scandir = os.path.join(studentdir, 'scans')
# .........................................................................
name2cwid = {
v['github'].lower():k
for k,v in students.students.items()
if 'github' in v
}
grades = {
cwid: OrderedDict( [
('extra credit', 0),
('overall', None),
('predictions', OrderedDict()),
] + [
((g,s,),OrderedDict())
for g,ss in standards.groups.items()
for s in ss
] )
for cwid in students.students
}
# .........................................................................
# from github
github = github3.GitHub()
try:
for r in sorted([ r.name for r in github.iter_user_repos(common.org) ]):
if r in ( 'course-materials', ): continue
assignment = 'a' + r[-2:]
for cwid in students.students:
grades[cwid][('assignment completion', '')][assignment] = None
for pr in github.iter_repo_issues(common.org, r, state='all'):
name = pr.user.login.lower()
if name not in name2cwid: continue
grades[name2cwid[name]] \
[('assignment completion', '')] \
[assignment] = True
with open(assignmentsfile, 'w') as f:
f.write(repr({
cwid: grades[cwid][('assignment completion', '')]
for cwid in grades
}))
except (requests.exceptions.ConnectionError, github3.models.GitHubError):
assignments = eval(open(assignmentsfile).read())
none = OrderedDict([
(a, None) for a in assignments[list(assignments.keys())[0]]
])
for cwid in grades:
if cwid in assignments:
grades[cwid][('assignment completion', '')] = assignments[cwid]
else:
grades[cwid][('assignment completion', '')] = none
# .........................................................................
# from scans
for d in sorted(os.listdir(scandir)):
if d.startswith('.'): continue
i = Namespace()
(i.date, i.assessment, i.standards) = d.split(',', maxsplit=2)
i.standards = [ standards.lookup(s) for s in i.standards.split(',') ]
for cwid in students.students:
for sta in i.standards:
grades[cwid][sta][i.assessment] = None
for f in os.listdir(os.path.join(scandir, d)):
if f.startswith('.'): continue
(i.name, i.scores) = \
f.split('.',maxsplit=1)[0].split(',', maxsplit=1)
i.scores = i.scores.split(',')
if '' in i.scores:
raise Error(
'WARNING: empty score in'
+ ' "' + os.path.join(d, f) + '"' )
if len(i.scores) != len(i.standards):
raise Error(
'WARNING: mismatch in number of scores for'
+ ' "' + os.path.join(d, f) + '"' )
i.scores = [
None if s == 'x' else
3.5 if s == '5' else
3.75 if s == '7' else
int(s)
for s in i.scores
]
for sta,sco in zip(i.standards,i.scores):
grades[students.lookup(i.name)][sta][i.assessment] = sco
# .........................................................................
# from file
private = common.importfile(os.path.join(studentdir, 'grades.py'))
for cwid in private.grades:
if cwid in grades: grades[cwid].update(private.grades[cwid])
else: grades[cwid] = private.grades[cwid]
# .........................................................................
for cwid in grades:
overall = 0
maximum = 0
for sta,assessments in grades[cwid].items():
if isinstance(sta, str): continue
scos = [ sco for sco in assessments.values() if sco is not None ]
if sta == ('assignment completion', ''):
sco = len(scos)/len(assessments) if len(assessments) > 0 else 0
assessments['overall'] = sco
overall += sco * standards.multipliers[sta]
maximum += standards.multipliers[sta]
continue
if len(scos) == 0:
assessments['overall'] = None
else:
if len(scos) == 1 or scos[-1] >= scos[-2]:
sco = scos[-1]
else: # scos[-1] < scos[-2]
sco = [ sco for sco in [1, 2, 3, 3.5, 3.75, 4]
if (scos[-1]+scos[-2])/2 <= sco ][0]
assessments['overall'] = sco
if sco >= 3:
overall += sco / 4 * standards.multipliers[sta]
maximum += standards.multipliers[sta]
ec = grades[cwid]['extra credit'] * 0.002
if grades[cwid]['overall'] is None:
grades[cwid]['overall'] = overall + ec
grades[cwid]['predictions']['current grade'] = grades[cwid]['overall']
if maximum == 0:
grades[cwid]['predictions']['average'] = None
grades[cwid]['predictions']['maximum without reassessing'] = None
else:
grades[cwid]['predictions']['average'] = overall / maximum
grades[cwid]['predictions']['maximum without reassessing'] = \
1 - maximum + overall + ec
# .........................................................................
return grades
def _gen_grades():
org = "2016-spring-csuf-benblazak-cpsc-121"
filedir = os.path.dirname(os.path.abspath(__file__))
if common.DEBUG:
studentdir = "./test/students"
else:
studentdir = "../../../students"
studentdir = os.path.abspath(os.path.join(filedir, studentdir))
assignmentsfile = os.path.join(studentdir, "assignments.gen.py")
scandir = os.path.join(studentdir, "scans")
# .........................................................................
name2cwid = {v["github"].lower(): k for k, v in students.students.items() if "github" in v}
grades = {
cwid: OrderedDict(
[("extra credit", 0), ("overall", None), ("predictions", OrderedDict())]
+ [((g, s), OrderedDict()) for g, ss in standards.groups.items() for s in ss]
)
for cwid in students.students
}
# .........................................................................
github = github3.GitHub()
try:
for r in sorted([r.name for r in github.iter_user_repos(org)]):
if r in ("course-materials",):
continue
assignment = "a" + r[-2:]
for cwid in students.students:
grades[cwid][("assignment completion", "")][assignment] = None
for pr in github.iter_repo_issues(org, r, state="all"):
name = pr.user.login
if name not in name2cwid:
continue
grades[name2cwid[name]][("assignment completion", "")][assignment] = 4
with open(assignmentsfile, "w") as f:
f.write(repr({cwid: grades[cwid][("assignment completion", "")] for cwid in grades}))
except (requests.exceptions.ConnectionError, github3.models.GitHubError):
assignments = eval(open(assignmentsfile).read())
none = OrderedDict([(a, None) for a in assignments[list(assignments.keys())[0]]])
for cwid in grades:
if cwid in assignments:
grades[cwid][("assignment completion", "")] = assignments[cwid]
else:
grades[cwid][("assignment completion", "")] = none
# .........................................................................
for d in sorted(os.listdir(scandir)):
if d.startswith("."):
continue
i = Namespace()
(i.date, i.assessment, i.standards) = d.split(",", maxsplit=2)
i.standards = [standards.lookup(s) for s in i.standards.split(",")]
for cwid in students.students:
for sta in i.standards:
grades[cwid][sta][i.assessment] = None
for f in os.listdir(os.path.join(scandir, d)):
if f.startswith("."):
continue
(i.name, i.scores) = f.split(".", maxsplit=1)[0].split(",", maxsplit=1)
i.scores = [
None if s == "" else 3.5 if s == "5" else 3.75 if s == "7" else int(s) for s in i.scores.split(",")
]
for sta, sco in zip(i.standards, i.scores):
grades[students.lookup(i.name)][sta][i.assessment] = sco
# .........................................................................
# TODO: update grades from other file
# .........................................................................
for cwid in grades:
overall = 0
maximum = 0
for sta, assessments in grades[cwid].items():
if isinstance(sta, str):
continue
scos = [sco for sco in assessments.values() if sco is not None]
if len(scos) == 0:
assessments["overall"] = sco
else:
if len(scos) == 1 or scos[-1] >= scos[-2]:
sco = scos[-1]
else: # scos[-1] < scos[-2]
sco = [sco for sco in [1, 2, 3, 3.5, 3.75, 4] if (scos[-1] + scos[-2]) / 2 <= sco][0]
assessments["overall"] = sco
overall += sco / 4 * standards.multipliers[sta]
maximum += standards.multipliers[sta]
ec = grades[cwid]["extra credit"] * 0.002
if grades[cwid]["overall"] is None:
grades[cwid]["overall"] = overall + ec
if maximum == 0:
grades[cwid]["predictions"]["average"] = None
grades[cwid]["predictions"]["maximum without reassessing"] = None
else:
grades[cwid]["predictions"]["average"] = overall / maximum
grades[cwid]["predictions"]["maximum without reassessing"] = 1 - maximum + overall + ec
# .........................................................................
# import pprint
# pprint.pprint(grades)
return grades
